PDB Short entry for 4BKX HEADER TRANSCRIPTION 30-APR-13 4BKX TITLE THE STRUCTURE OF HDAC1 IN COMPLEX WITH THE DIMERIC ELM2-SANT DOMAIN OF TITLE 2 MTA1 FROM THE NURD COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: METASTASIS-ASSOCIATED PROTEIN MTA1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ELM2-SANT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE DEACETYLASE 1; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: HD1; COMPND 10 EC: 3.5.1.98; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PCDNA3; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PCDNA3 KEYWDS TRANSCRIPTION, INOSITOL PHOSPHATE SIGNALLING, ELM2-SANT DOMAIN, HDAC, KEYWDS 2 HDAC1, HISTONE DEACETYLASE, MTA1 EXPDTA X-RAY DIFFRACTION AUTHOR C.J.MILLARD,P.J.WATSON,I.CELARDO,Y.GORDIYENKO,S.M.COWLEY, AUTHOR 2 C.V.ROBINSON,L.FAIRALL,J.W.R.SCHWABE REVDAT 3 20-DEC-23 4BKX 1 REMARK LINK REVDAT 2 31-JUL-13 4BKX 1 JRNL REVDAT 1 03-JUL-13 4BKX 0 JRNL AUTH C.J.MILLARD,P.J.WATSON,I.CELARDO,Y.GORDIYENKO,S.M.COWLEY, JRNL AUTH 2 C.V.ROBINSON,L.FAIRALL,J.W.R.SCHWABE JRNL TITL CLASS I HDACS SHARE A COMMON MECHANISM OF REGULATION BY JRNL TITL 2 INOSITOL PHOSPHATES. JRNL REF MOL.CELL V. 51 57 2013 JRNL REFN ISSN 1097-2765 JRNL PMID 23791785 JRNL DOI 10.1016/J.MOLCEL.2013.05.020 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 16916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 910 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1261 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4235 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : 0.50000 REMARK 3 B33 (A**2) : -1.61000 REMARK 3 B12 (A**2) : 0.50000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.406 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.300 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.180 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4357 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5896 ; 1.023 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 527 ; 6.830 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 217 ;36.692 ;24.055 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 722 ;16.653 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.694 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 623 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3358 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4BKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-APR-13. REMARK 100 THE DEPOSITION ID IS D_1290056690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16916 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 76.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4A69 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA HEPES PH7.5, 2M AMMONIUM REMARK 280 SULPHATE, 5% PEG400 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.77600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.38800 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.38800 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.77600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: DIMER OF A HETERODIMERIC COMPLEX REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -277.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 -162.29850 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 93.70308 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 160 REMARK 465 ALA A 161 REMARK 465 ALA A 162 REMARK 465 ASP A 163 REMARK 465 LYS A 164 REMARK 465 CYS A 229 REMARK 465 SER A 230 REMARK 465 SER A 231 REMARK 465 SER A 232 REMARK 465 VAL A 233 REMARK 465 ARG A 234 REMARK 465 GLN A 235 REMARK 465 PRO A 236 REMARK 465 ASP A 334 REMARK 465 ARG A 335 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 THR B 4 REMARK 465 GLN B 5 REMARK 465 GLY B 6 REMARK 465 THR B 7 REMARK 465 PRO B 377 REMARK 465 GLY B 378 REMARK 465 VAL B 379 REMARK 465 GLN B 380 REMARK 465 MET B 381 REMARK 465 GLN B 382 REMARK 465 ALA B 383 REMARK 465 ILE B 384 REMARK 465 PRO B 385 REMARK 465 GLU B 386 REMARK 465 ASP B 387 REMARK 465 ALA B 388 REMARK 465 ILE B 389 REMARK 465 PRO B 390 REMARK 465 GLU B 391 REMARK 465 GLU B 392 REMARK 465 SER B 393 REMARK 465 GLY B 394 REMARK 465 ASP B 395 REMARK 465 GLU B 396 REMARK 465 ASP B 397 REMARK 465 GLU B 398 REMARK 465 ASP B 399 REMARK 465 ASP B 400 REMARK 465 PRO B 401 REMARK 465 ASP B 402 REMARK 465 LYS B 403 REMARK 465 ARG B 404 REMARK 465 ILE B 405 REMARK 465 SER B 406 REMARK 465 ILE B 407 REMARK 465 CYS B 408 REMARK 465 SER B 409 REMARK 465 SER B 410 REMARK 465 ASP B 411 REMARK 465 LYS B 412 REMARK 465 ARG B 413 REMARK 465 ILE B 414 REMARK 465 ALA B 415 REMARK 465 CYS B 416 REMARK 465 GLU B 417 REMARK 465 GLU B 418 REMARK 465 GLU B 419 REMARK 465 PHE B 420 REMARK 465 SER B 421 REMARK 465 ASP B 422 REMARK 465 SER B 423 REMARK 465 GLU B 424 REMARK 465 GLU B 425 REMARK 465 GLU B 426 REMARK 465 GLY B 427 REMARK 465 GLU B 428 REMARK 465 GLY B 429 REMARK 465 GLY B 430 REMARK 465 ARG B 431 REMARK 465 LYS B 432 REMARK 465 ASN B 433 REMARK 465 SER B 434 REMARK 465 SER B 435 REMARK 465 ASN B 436 REMARK 465 PHE B 437 REMARK 465 LYS B 438 REMARK 465 LYS B 439 REMARK 465 ALA B 440 REMARK 465 LYS B 441 REMARK 465 ARG B 442 REMARK 465 VAL B 443 REMARK 465 LYS B 444 REMARK 465 THR B 445 REMARK 465 GLU B 446 REMARK 465 ASP B 447 REMARK 465 GLU B 448 REMARK 465 LYS B 449 REMARK 465 GLU B 450 REMARK 465 LYS B 451 REMARK 465 ASP B 452 REMARK 465 PRO B 453 REMARK 465 GLU B 454 REMARK 465 GLU B 455 REMARK 465 LYS B 456 REMARK 465 LYS B 457 REMARK 465 GLU B 458 REMARK 465 VAL B 459 REMARK 465 THR B 460 REMARK 465 GLU B 461 REMARK 465 GLU B 462 REMARK 465 GLU B 463 REMARK 465 LYS B 464 REMARK 465 THR B 465 REMARK 465 LYS B 466 REMARK 465 GLU B 467 REMARK 465 GLU B 468 REMARK 465 LYS B 469 REMARK 465 PRO B 470 REMARK 465 GLU B 471 REMARK 465 ALA B 472 REMARK 465 LYS B 473 REMARK 465 GLY B 474 REMARK 465 VAL B 475 REMARK 465 LYS B 476 REMARK 465 GLU B 477 REMARK 465 GLU B 478 REMARK 465 VAL B 479 REMARK 465 LYS B 480 REMARK 465 LEU B 481 REMARK 465 ALA B 482 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 239 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 ARG B 80 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 89 CG CD CE NZ REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 ASN B 349 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE B 205 C PHE B 205 O -0.119 REMARK 500 PHE B 205 C PRO B 206 N 0.269 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE B 205 CA - C - N ANGL. DEV. = -17.8 DEGREES REMARK 500 PHE B 205 O - C - N ANGL. DEV. = 13.2 DEGREES REMARK 500 PRO B 206 C - N - CA ANGL. DEV. = -18.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 173 -44.75 -132.31 REMARK 500 LEU A 227 31.82 -86.84 REMARK 500 TYR B 67 -48.21 -137.65 REMARK 500 SER B 88 -27.86 -39.09 REMARK 500 GLU B 98 -68.91 -135.04 REMARK 500 PRO B 206 12.41 -144.91 REMARK 500 CYS B 261 58.64 -103.99 REMARK 500 CYS B 273 34.64 -142.46 REMARK 500 PRO B 294 109.99 -45.25 REMARK 500 ASP B 321 46.10 33.89 REMARK 500 PHE B 334 -39.45 -39.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE B 205 PRO B 206 69.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE B 205 18.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 602 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 174 OD1 REMARK 620 2 ASP B 174 O 65.5 REMARK 620 3 ASP B 176 O 90.5 99.1 REMARK 620 4 HIS B 178 O 85.3 149.9 72.3 REMARK 620 5 SER B 197 OG 111.1 91.4 158.4 107.0 REMARK 620 6 PHE B 198 O 134.5 78.8 67.6 121.1 96.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 600 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 176 OD1 REMARK 620 2 HIS B 178 ND1 114.9 REMARK 620 3 ASP B 264 OD2 102.1 98.4 REMARK 620 4 ACT B 601 O 91.8 109.6 139.9 REMARK 620 5 ACT B 601 OXT 141.2 94.4 97.7 53.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 603 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 187 O REMARK 620 2 VAL B 193 O 99.5 REMARK 620 3 TYR B 222 O 174.2 75.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 504 DBREF 4BKX A 162 335 UNP Q13330 MTA1_HUMAN 162 335 DBREF 4BKX B 1 482 UNP Q13547 HDAC1_HUMAN 1 482 SEQADV 4BKX GLY A 160 UNP Q13330 EXPRESSION TAG SEQADV 4BKX ALA A 161 UNP Q13330 EXPRESSION TAG SEQRES 1 A 176 GLY ALA ALA ASP LYS GLY GLU ILE ARG VAL GLY ASN ARG SEQRES 2 A 176 TYR GLN ALA ASP ILE THR ASP LEU LEU LYS GLU GLY GLU SEQRES 3 A 176 GLU ASP GLY ARG ASP GLN SER ARG LEU GLU THR GLN VAL SEQRES 4 A 176 TRP GLU ALA HIS ASN PRO LEU THR ASP LYS GLN ILE ASP SEQRES 5 A 176 GLN PHE LEU VAL VAL ALA ARG SER VAL GLY THR PHE ALA SEQRES 6 A 176 ARG ALA LEU ASP CYS SER SER SER VAL ARG GLN PRO SER SEQRES 7 A 176 LEU HIS MET SER ALA ALA ALA ALA SER ARG ASP ILE THR SEQRES 8 A 176 LEU PHE HIS ALA MET ASP THR LEU HIS LYS ASN ILE TYR SEQRES 9 A 176 ASP ILE SER LYS ALA ILE SER ALA LEU VAL PRO GLN GLY SEQRES 10 A 176 GLY PRO VAL LEU CYS ARG ASP GLU MET GLU GLU TRP SER SEQRES 11 A 176 ALA SER GLU ALA ASN LEU PHE GLU GLU ALA LEU GLU LYS SEQRES 12 A 176 TYR GLY LYS ASP PHE THR ASP ILE GLN GLN ASP PHE LEU SEQRES 13 A 176 PRO TRP LYS SER LEU THR SER ILE ILE GLU TYR TYR TYR SEQRES 14 A 176 MET TRP LYS THR THR ASP ARG SEQRES 1 B 482 MET ALA GLN THR GLN GLY THR ARG ARG LYS VAL CYS TYR SEQRES 2 B 482 TYR TYR ASP GLY ASP VAL GLY ASN TYR TYR TYR GLY GLN SEQRES 3 B 482 GLY HIS PRO MET LYS PRO HIS ARG ILE ARG MET THR HIS SEQRES 4 B 482 ASN LEU LEU LEU ASN TYR GLY LEU TYR ARG LYS MET GLU SEQRES 5 B 482 ILE TYR ARG PRO HIS LYS ALA ASN ALA GLU GLU MET THR SEQRES 6 B 482 LYS TYR HIS SER ASP ASP TYR ILE LYS PHE LEU ARG SER SEQRES 7 B 482 ILE ARG PRO ASP ASN MET SER GLU TYR SER LYS GLN MET SEQRES 8 B 482 GLN ARG PHE ASN VAL GLY GLU ASP CYS PRO VAL PHE ASP SEQRES 9 B 482 GLY LEU PHE GLU PHE CYS GLN LEU SER THR GLY GLY SER SEQRES 10 B 482 VAL ALA SER ALA VAL LYS LEU ASN LYS GLN GLN THR ASP SEQRES 11 B 482 ILE ALA VAL ASN TRP ALA GLY GLY LEU HIS HIS ALA LYS SEQRES 12 B 482 LYS SER GLU ALA SER GLY PHE CYS TYR VAL ASN ASP ILE SEQRES 13 B 482 VAL LEU ALA ILE LEU GLU LEU LEU LYS TYR HIS GLN ARG SEQRES 14 B 482 VAL LEU TYR ILE ASP ILE ASP ILE HIS HIS GLY ASP GLY SEQRES 15 B 482 VAL GLU GLU ALA PHE TYR THR THR ASP ARG VAL MET THR SEQRES 16 B 482 VAL SER PHE HIS LYS TYR GLY GLU TYR PHE PRO GLY THR SEQRES 17 B 482 GLY ASP LEU ARG ASP ILE GLY ALA GLY LYS GLY LYS TYR SEQRES 18 B 482 TYR ALA VAL ASN TYR PRO LEU ARG ASP GLY ILE ASP ASP SEQRES 19 B 482 GLU SER TYR GLU ALA ILE PHE LYS PRO VAL MET SER LYS SEQRES 20 B 482 VAL MET GLU MET PHE GLN PRO SER ALA VAL VAL LEU GLN SEQRES 21 B 482 CYS GLY SER ASP SER LEU SER GLY ASP ARG LEU GLY CYS SEQRES 22 B 482 PHE ASN LEU THR ILE LYS GLY HIS ALA LYS CYS VAL GLU SEQRES 23 B 482 PHE VAL LYS SER PHE ASN LEU PRO MET LEU MET LEU GLY SEQRES 24 B 482 GLY GLY GLY TYR THR ILE ARG ASN VAL ALA ARG CYS TRP SEQRES 25 B 482 THR TYR GLU THR ALA VAL ALA LEU ASP THR GLU ILE PRO SEQRES 26 B 482 ASN GLU LEU PRO TYR ASN ASP TYR PHE GLU TYR PHE GLY SEQRES 27 B 482 PRO ASP PHE LYS LEU HIS ILE SER PRO SER ASN MET THR SEQRES 28 B 482 ASN GLN ASN THR ASN GLU TYR LEU GLU LYS ILE LYS GLN SEQRES 29 B 482 ARG LEU PHE GLU ASN LEU ARG MET LEU PRO HIS ALA PRO SEQRES 30 B 482 GLY VAL GLN MET GLN ALA ILE PRO GLU ASP ALA ILE PRO SEQRES 31 B 482 GLU GLU SER GLY ASP GLU ASP GLU ASP ASP PRO ASP LYS SEQRES 32 B 482 ARG ILE SER ILE CYS SER SER ASP LYS ARG ILE ALA CYS SEQRES 33 B 482 GLU GLU GLU PHE SER ASP SER GLU GLU GLU GLY GLU GLY SEQRES 34 B 482 GLY ARG LYS ASN SER SER ASN PHE LYS LYS ALA LYS ARG SEQRES 35 B 482 VAL LYS THR GLU ASP GLU LYS GLU LYS ASP PRO GLU GLU SEQRES 36 B 482 LYS LYS GLU VAL THR GLU GLU GLU LYS THR LYS GLU GLU SEQRES 37 B 482 LYS PRO GLU ALA LYS GLY VAL LYS GLU GLU VAL LYS LEU SEQRES 38 B 482 ALA HET ZN B 600 1 HET ACT B 601 4 HET K B 602 1 HET K B 603 1 HET SO4 B 501 5 HET SO4 B 502 5 HET SO4 B 503 5 HET SO4 B 504 5 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM K POTASSIUM ION HETNAM SO4 SULFATE ION FORMUL 3 ZN ZN 2+ FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 K 2(K 1+) FORMUL 7 SO4 4(O4 S 2-) HELIX 1 1 THR A 206 ARG A 225 1 20 HELIX 2 2 SER A 237 ARG A 247 1 11 HELIX 3 3 ARG A 247 ASN A 261 1 15 HELIX 4 4 ASP A 264 VAL A 273 1 10 HELIX 5 5 ASP A 283 TRP A 288 1 6 HELIX 6 6 SER A 289 GLY A 304 1 16 HELIX 7 7 ASP A 306 PHE A 314 1 9 HELIX 8 8 SER A 319 LYS A 331 1 13 HELIX 9 9 ASP B 18 TYR B 22 5 5 HELIX 10 10 PRO B 32 TYR B 45 1 14 HELIX 11 11 LEU B 47 MET B 51 5 5 HELIX 12 12 ASN B 60 THR B 65 1 6 HELIX 13 13 SER B 69 ILE B 79 1 11 HELIX 14 14 TYR B 87 ASN B 95 1 9 HELIX 15 15 GLY B 105 LYS B 126 1 22 HELIX 16 16 ASN B 154 LEU B 164 1 11 HELIX 17 17 GLY B 180 PHE B 187 1 8 HELIX 18 18 ALA B 216 LYS B 220 5 5 HELIX 19 19 ASP B 233 GLN B 253 1 21 HELIX 20 20 GLY B 262 SER B 265 5 4 HELIX 21 21 THR B 277 SER B 290 1 14 HELIX 22 22 THR B 304 LEU B 320 1 17 HELIX 23 23 TYR B 333 PHE B 337 5 5 HELIX 24 24 THR B 355 MET B 372 1 18 SHEET 1 AA 9 GLU A 195 TRP A 199 0 SHEET 2 AA 9 GLU B 52 PRO B 56 -1 O ILE B 53 N VAL A 198 SHEET 3 AA 9 VAL B 11 TYR B 14 1 O VAL B 11 N GLU B 52 SHEET 4 AA 9 ILE B 131 ASN B 134 1 O ILE B 131 N CYS B 12 SHEET 5 AA 9 MET B 295 LEU B 298 1 O MET B 295 N ALA B 132 SHEET 6 AA 9 ALA B 256 GLN B 260 1 O VAL B 257 N LEU B 296 SHEET 7 AA 9 VAL B 170 ASP B 174 1 O LEU B 171 N VAL B 258 SHEET 8 AA 9 VAL B 193 LYS B 200 1 O MET B 194 N TYR B 172 SHEET 9 AA 9 ALA B 223 LEU B 228 1 O VAL B 224 N SER B 197 LINK OD1 ASP B 174 K K B 602 1555 1555 2.75 LINK O ASP B 174 K K B 602 1555 1555 3.08 LINK OD1 ASP B 176 ZN ZN B 600 1555 1555 1.96 LINK O ASP B 176 K K B 602 1555 1555 2.56 LINK ND1 HIS B 178 ZN ZN B 600 1555 1555 2.28 LINK O HIS B 178 K K B 602 1555 1555 3.10 LINK O PHE B 187 K K B 603 1555 1555 2.77 LINK O VAL B 193 K K B 603 1555 1555 3.23 LINK OG SER B 197 K K B 602 1555 1555 2.93 LINK O PHE B 198 K K B 602 1555 1555 3.13 LINK O TYR B 222 K K B 603 1555 1555 3.24 LINK OD2 ASP B 264 ZN ZN B 600 1555 1555 1.95 LINK ZN ZN B 600 O ACT B 601 1555 1555 2.50 LINK ZN ZN B 600 OXT ACT B 601 1555 1555 2.35 SITE 1 AC1 4 ASP B 176 HIS B 178 ASP B 264 ACT B 601 SITE 1 AC2 8 HIS B 140 HIS B 141 ASP B 176 HIS B 178 SITE 2 AC2 8 ASP B 264 GLY B 301 TYR B 303 ZN B 600 SITE 1 AC3 5 ASP B 174 ASP B 176 HIS B 178 SER B 197 SITE 2 AC3 5 PHE B 198 SITE 1 AC4 4 PHE B 187 THR B 190 VAL B 193 TYR B 222 SITE 1 AC5 5 ARG B 270 TYR B 303 THR B 304 ILE B 305 SITE 2 AC5 5 ARG B 306 SITE 1 AC6 6 LYS A 305 TYR A 327 TYR A 328 LYS A 331 SITE 2 AC6 6 LYS B 31 SO4 B 503 SITE 1 AC7 5 LYS A 305 GLY B 27 HIS B 28 LYS B 31 SITE 2 AC7 5 SO4 B 502 SITE 1 AC8 3 ARG B 55 HIS B 57 LYS B 58 CRYST1 108.199 108.199 133.164 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009242 0.005336 0.000000 0.00000 SCALE2 0.000000 0.010672 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007510 0.00000