PDB Short entry for 3NYJ HEADER PROTEIN FIBRIL 15-JUL-10 3NYJ TITLE CRYSTAL STRUCTURE ANALYSIS OF APP E2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALZHEIMER DISEASE AMYLOID PROTEIN, ABPP, APPI, APP, PREA4, COMPND 5 CEREBRAL VASCULAR AMYLOID PEPTIDE, CVAP, PROTEASE NEXIN-II, PN-II, N- COMPND 6 APP, SOLUBLE APP-ALPHA, S-APP-ALPHA, SOLUBLE APP-BETA, S-APP-BETA, COMPND 7 C99, BETA-AMYLOID PROTEIN 42, BETA-APP42, BETA-AMYLOID PROTEIN 40, COMPND 8 BETA-APP40, C83, P3(42), P3(40), C80, GAMMA-SECRETASE C-TERMINAL COMPND 9 FRAGMENT 59, GAMMA-CTF(59), AMYLOID INTRACELLULAR DOMAIN 59, AICD-59, COMPND 10 AID(59), GAMMA-SECRETASE C-TERMINAL FRAGMENT 57, GAMMA-CTF(57), COMPND 11 AMYLOID INTRACELLULAR DOMAIN 57, AICD-57, AID(57), GAMMA-SECRETASE C- COMPND 12 TERMINAL FRAGMENT 50, GAMMA-CTF(50), AMYLOID INTRACELLULAR DOMAIN 50, COMPND 13 AICD-50, AID(50), C31; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: A4, AD1, APP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS ALZHEIMER'S DISEASE, HELICAL HAIRPIN, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR Y.HA,J.HU,S.LEE,X.LIU REVDAT 3 08-NOV-17 3NYJ 1 REMARK REVDAT 2 29-JUN-11 3NYJ 1 JRNL REVDAT 1 01-JUN-11 3NYJ 0 JRNL AUTH S.LEE,Y.XUE,J.HU,Y.WANG,X.LIU,B.DEMELER,Y.HA JRNL TITL THE E2 DOMAINS OF APP AND APLP1 SHARE A CONSERVED MODE OF JRNL TITL 2 DIMERIZATION. JRNL REF BIOCHEMISTRY V. 50 5453 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21574595 JRNL DOI 10.1021/BI101846X REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 4888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.297 REMARK 3 FREE R VALUE : 0.380 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 515 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1226 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 102.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NYJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.14 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4888 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.08100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 20% ISOPROPANOL, 0.1M NA REMARK 280 CITRATE, PH 5.6, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 57.48950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.07450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.48950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.07450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -1.000000 0.000000 0.000000 -114.97900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 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 342 REMARK 465 SER A 343 REMARK 465 HIS A 344 REMARK 465 MSE A 345 REMARK 465 PRO A 346 REMARK 465 THR A 347 REMARK 465 THR A 348 REMARK 465 ALA A 349 REMARK 465 ALA A 350 REMARK 465 SER A 351 REMARK 465 THR A 352 REMARK 465 PRO A 353 REMARK 465 ASP A 354 REMARK 465 ALA A 355 REMARK 465 VAL A 356 REMARK 465 ASP A 357 REMARK 465 LYS A 358 REMARK 465 TYR A 359 REMARK 465 ASP A 541 REMARK 465 GLU A 542 REMARK 465 VAL A 543 REMARK 465 ASP A 544 REMARK 465 GLU A 545 REMARK 465 LEU A 546 REMARK 465 LEU A 547 REMARK 465 GLN A 548 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 LEU A 360 CG CD1 CD2 REMARK 470 GLU A 361 CG CD OE1 OE2 REMARK 470 THR A 362 OG1 CG2 REMARK 470 HIS A 371 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 373 CG CD OE1 NE2 REMARK 470 LYS A 374 CD CE NZ REMARK 470 GLU A 377 CG CD OE1 OE2 REMARK 470 GLU A 380 CG CD OE1 OE2 REMARK 470 LYS A 382 CD CE NZ REMARK 470 HIS A 383 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 384 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 386 CD NE CZ NH1 NH2 REMARK 470 ARG A 392 CD NE CZ NH1 NH2 REMARK 470 ARG A 399 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 400 CG CD OE1 NE2 REMARK 470 LYS A 402 CG CD CE NZ REMARK 470 ASN A 403 CG OD1 ND2 REMARK 470 LYS A 406 CG CD CE NZ REMARK 470 ASP A 408 CG OD1 OD2 REMARK 470 LYS A 409 CD CE NZ REMARK 470 LYS A 410 CD CE NZ REMARK 470 GLN A 417 CG CD OE1 NE2 REMARK 470 GLU A 418 CG CD OE1 OE2 REMARK 470 GLU A 421 CG CD OE1 OE2 REMARK 470 GLU A 424 CG CD OE1 OE2 REMARK 470 GLN A 425 CG CD OE1 NE2 REMARK 470 GLU A 426 CG CD OE1 OE2 REMARK 470 GLU A 430 CG CD OE1 OE2 REMARK 470 GLN A 433 CG CD OE1 NE2 REMARK 470 GLU A 436 CG CD OE1 OE2 REMARK 470 MSE A 439 CG SE CE REMARK 470 GLU A 443 CG CD OE1 OE2 REMARK 470 ARG A 449 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 451 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 452 CG CD1 CD2 REMARK 470 LEU A 454 CG CD1 CD2 REMARK 470 GLU A 455 CG CD OE1 OE2 REMARK 470 ILE A 458 CG1 CG2 CD1 REMARK 470 LEU A 461 CG CD1 CD2 REMARK 470 GLN A 462 CG CD OE1 NE2 REMARK 470 VAL A 464 CG1 CG2 REMARK 470 ARG A 467 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 470 ND1 CD2 CE1 NE2 REMARK 470 VAL A 471 CG1 CG2 REMARK 470 PHE A 472 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 473 CG OD1 ND2 REMARK 470 LEU A 475 CG CD1 CD2 REMARK 470 LYS A 476 CG CD CE NZ REMARK 470 LYS A 477 CG CD CE NZ REMARK 470 LYS A 484 CG CD CE NZ REMARK 470 LYS A 491 CG CD CE NZ REMARK 470 PHE A 493 CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 494 CG CD OE1 OE2 REMARK 470 HIS A 495 ND1 CD2 CE1 NE2 REMARK 470 VAL A 496 CG1 CG2 REMARK 470 MSE A 498 CG SE CE REMARK 470 VAL A 499 CG1 CG2 REMARK 470 ASP A 500 CG OD1 OD2 REMARK 470 LYS A 502 CG CD CE NZ REMARK 470 LYS A 503 CG CD CE NZ REMARK 470 ILE A 507 CG1 CG2 CD1 REMARK 470 ARG A 508 CG CD NE CZ NH1 NH2 REMARK 470 SER A 509 OG REMARK 470 VAL A 511 CG1 CG2 REMARK 470 LEU A 515 CD1 CD2 REMARK 470 ARG A 516 CD NE CZ NH1 NH2 REMARK 470 GLU A 520 CG CD OE1 OE2 REMARK 470 GLN A 524 CG CD OE1 NE2 REMARK 470 TYR A 530 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 531 CG OD1 ND2 REMARK 470 VAL A 532 CG1 CG2 REMARK 470 GLU A 537 CG CD OE1 OE2 REMARK 470 GLU A 538 CG CD OE1 OE2 REMARK 470 ILE A 539 CG1 CG2 CD1 REMARK 470 GLN A 540 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PRO A 465 N ARG A 467 2.11 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 PRO A 363 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO A 465 C - N - CA ANGL. DEV. = -9.1 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 THR A 362 -67.92 -130.65 REMARK 500 PRO A 363 133.11 16.98 REMARK 500 ASP A 365 105.69 -50.72 REMARK 500 GLU A 366 -77.88 -24.67 REMARK 500 ALA A 370 -72.42 -52.66 REMARK 500 ARG A 399 -3.53 -56.94 REMARK 500 ALA A 401 9.65 -67.70 REMARK 500 PRO A 405 163.42 -47.98 REMARK 500 ALA A 428 -81.46 -49.88 REMARK 500 THR A 459 -2.52 -59.99 REMARK 500 ALA A 460 -124.92 30.67 REMARK 500 LEU A 461 49.97 -159.78 REMARK 500 ALA A 463 157.99 166.45 REMARK 500 VAL A 464 -100.76 9.16 REMARK 500 PRO A 466 59.45 -36.44 REMARK 500 ARG A 467 67.27 13.67 REMARK 500 VAL A 479 -78.07 -48.62 REMARK 500 ASP A 485 -70.21 -58.46 REMARK 500 LYS A 491 -72.08 -43.00 REMARK 500 HIS A 492 -50.18 -29.66 REMARK 500 MSE A 498 -94.92 -74.73 REMARK 500 VAL A 499 -57.96 -20.60 REMARK 500 PRO A 501 -37.96 -38.14 REMARK 500 ILE A 507 6.19 -64.97 REMARK 500 HIS A 514 -72.11 -49.45 REMARK 500 ARG A 521 -70.87 -55.60 REMARK 500 MSE A 522 -70.98 -32.41 REMARK 500 SER A 527 13.22 -67.50 REMARK 500 ALA A 534 -71.30 -45.61 REMARK 500 ALA A 536 -84.81 -54.48 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 OS A 1 OS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 9 O REMARK 620 2 HOH A 4 O 120.2 REMARK 620 3 HOH A 27 O 89.3 119.2 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 OS A 1 DBREF 3NYJ A 346 548 UNP P05067 A4_HUMAN 365 567 SEQADV 3NYJ GLY A 342 UNP P05067 EXPRESSION TAG SEQADV 3NYJ SER A 343 UNP P05067 EXPRESSION TAG SEQADV 3NYJ HIS A 344 UNP P05067 EXPRESSION TAG SEQADV 3NYJ MSE A 345 UNP P05067 EXPRESSION TAG SEQRES 1 A 207 GLY SER HIS MSE PRO THR THR ALA ALA SER THR PRO ASP SEQRES 2 A 207 ALA VAL ASP LYS TYR LEU GLU THR PRO GLY ASP GLU ASN SEQRES 3 A 207 GLU HIS ALA HIS PHE GLN LYS ALA LYS GLU ARG LEU GLU SEQRES 4 A 207 ALA LYS HIS ARG GLU ARG MSE SER GLN VAL MSE ARG GLU SEQRES 5 A 207 TRP GLU GLU ALA GLU ARG GLN ALA LYS ASN LEU PRO LYS SEQRES 6 A 207 ALA ASP LYS LYS ALA VAL ILE GLN HIS PHE GLN GLU LYS SEQRES 7 A 207 VAL GLU SER LEU GLU GLN GLU ALA ALA ASN GLU ARG GLN SEQRES 8 A 207 GLN LEU VAL GLU THR HIS MSE ALA ARG VAL GLU ALA MSE SEQRES 9 A 207 LEU ASN ASP ARG ARG ARG LEU ALA LEU GLU ASN TYR ILE SEQRES 10 A 207 THR ALA LEU GLN ALA VAL PRO PRO ARG PRO ARG HIS VAL SEQRES 11 A 207 PHE ASN MSE LEU LYS LYS TYR VAL ARG ALA GLU GLN LYS SEQRES 12 A 207 ASP ARG GLN HIS THR LEU LYS HIS PHE GLU HIS VAL ARG SEQRES 13 A 207 MSE VAL ASP PRO LYS LYS ALA ALA GLN ILE ARG SER GLN SEQRES 14 A 207 VAL MSE THR HIS LEU ARG VAL ILE TYR GLU ARG MSE ASN SEQRES 15 A 207 GLN SER LEU SER LEU LEU TYR ASN VAL PRO ALA VAL ALA SEQRES 16 A 207 GLU GLU ILE GLN ASP GLU VAL ASP GLU LEU LEU GLN MODRES 3NYJ MSE A 387 MET SELENOMETHIONINE MODRES 3NYJ MSE A 391 MET SELENOMETHIONINE MODRES 3NYJ MSE A 439 MET SELENOMETHIONINE MODRES 3NYJ MSE A 445 MET SELENOMETHIONINE MODRES 3NYJ MSE A 474 MET SELENOMETHIONINE MODRES 3NYJ MSE A 498 MET SELENOMETHIONINE MODRES 3NYJ MSE A 512 MET SELENOMETHIONINE MODRES 3NYJ MSE A 522 MET SELENOMETHIONINE HET MSE A 387 8 HET MSE A 391 8 HET MSE A 439 5 HET MSE A 445 8 HET MSE A 474 8 HET MSE A 498 5 HET MSE A 512 8 HET MSE A 522 8 HET OS A 1 1 HETNAM MSE SELENOMETHIONINE HETNAM OS OSMIUM ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 OS OS 3+ FORMUL 3 HOH *36(H2 O) HELIX 1 1 ASN A 367 ARG A 399 1 33 HELIX 2 2 PRO A 405 THR A 459 1 55 HELIX 3 3 ARG A 467 ASP A 500 1 34 HELIX 4 4 ASP A 500 SER A 527 1 28 HELIX 5 5 LEU A 528 VAL A 532 5 5 HELIX 6 6 PRO A 533 GLN A 540 1 8 LINK C ARG A 386 N MSE A 387 1555 1555 1.33 LINK C MSE A 387 N SER A 388 1555 1555 1.33 LINK C VAL A 390 N MSE A 391 1555 1555 1.33 LINK C MSE A 391 N ARG A 392 1555 1555 1.33 LINK C ALA A 444 N MSE A 445 1555 1555 1.32 LINK C MSE A 445 N LEU A 446 1555 1555 1.33 LINK C MSE A 512 N THR A 513 1555 1555 1.33 LINK C ARG A 521 N MSE A 522 1555 1555 1.33 LINK C MSE A 522 N ASN A 523 1555 1555 1.33 LINK OS OS A 1 O HOH A 9 1555 1555 2.47 LINK OS OS A 1 O HOH A 4 1555 1555 2.56 LINK OS OS A 1 O HOH A 27 1555 1555 2.63 LINK C HIS A 438 N MSE A 439 1555 1555 1.34 LINK C MSE A 439 N ALA A 440 1555 1555 1.33 LINK C ASN A 473 N MSE A 474 1555 1555 1.33 LINK C MSE A 474 N LEU A 475 1555 1555 1.33 LINK C ARG A 497 N MSE A 498 1555 1555 1.33 LINK C MSE A 498 N VAL A 499 1555 1555 1.33 LINK C VAL A 511 N MSE A 512 1555 1555 1.33 SITE 1 AC1 3 HOH A 4 HOH A 9 HOH A 27 CRYST1 114.979 40.149 58.376 90.00 90.00 90.00 P 21 21 2 4 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 0.008697 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017130 0.00000