PDB Short entry for 3G6U HEADER TRANSCRIPTION/DNA 08-FEB-09 3G6U TITLE GR DNA-BINDING DOMAIN:FKBP5 16BP COMPLEX-49 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOCORTICOID RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 440-525; COMPND 5 SYNONYM: GR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*TP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*T)- COMPND 9 3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: FKBP BOTTOM STRAND; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*T)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: FKBP TOP STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GRL, NR3C1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS GLUCOCORTICOID, DNA-BINDING, ALLOSTERY, LEVER ARM, TRANSCRIPTION, KEYWDS 2 HORMONE, ALTERNATIVE INITIATION, CHROMATIN REGULATOR, CYTOPLASM, KEYWDS 3 LIPID-BINDING, METAL-BINDING, NUCLEUS, PHOSPHOPROTEIN, POLYMORPHISM, KEYWDS 4 RECEPTOR, STEROID-BINDING, TRANSCRIPTION REGULATION, UBL KEYWDS 5 CONJUGATION, ZINC, ZINC-FINGER, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.A.PUFALL,K.R.YAMAMOTO,S.H.MEIJSING REVDAT 4 06-SEP-23 3G6U 1 REMARK SEQADV REVDAT 3 01-NOV-17 3G6U 1 REMARK REVDAT 2 02-JUN-09 3G6U 1 JRNL REVDAT 1 21-APR-09 3G6U 0 JRNL AUTH S.H.MEIJSING,M.A.PUFALL,A.Y.SO,D.L.BATES,L.CHEN,K.R.YAMAMOTO JRNL TITL DNA BINDING SITE SEQUENCE DIRECTS GLUCOCORTICOID RECEPTOR JRNL TITL 2 STRUCTURE AND ACTIVITY. JRNL REF SCIENCE V. 324 407 2009 JRNL REFN ISSN 0036-8075 JRNL PMID 19372434 JRNL DOI 10.1126/SCIENCE.1164265 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 25112 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.270 REMARK 3 FREE R VALUE TEST SET COUNT : 1825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.3804 - 4.0954 0.99 2762 223 0.1715 0.1975 REMARK 3 2 4.0954 - 3.2514 0.99 2660 210 0.1811 0.2177 REMARK 3 3 3.2514 - 2.8406 0.97 2604 205 0.2001 0.2444 REMARK 3 4 2.8406 - 2.5810 0.95 2537 192 0.1958 0.2289 REMARK 3 5 2.5810 - 2.3961 0.93 2479 203 0.1903 0.2071 REMARK 3 6 2.3961 - 2.2548 0.90 2399 188 0.1822 0.2485 REMARK 3 7 2.2548 - 2.1419 0.87 2318 179 0.2011 0.2153 REMARK 3 8 2.1419 - 2.0487 0.84 2213 171 0.2036 0.2311 REMARK 3 9 2.0487 - 1.9698 0.72 1901 146 0.2344 0.3054 REMARK 3 10 1.9698 - 1.9000 0.53 1414 108 0.2618 0.2880 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 82.81 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.18 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 NULL REMARK 3 ANGLE : 1.507 NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 12.4627 -16.8882 41.0854 REMARK 3 T TENSOR REMARK 3 T11: 0.2497 T22: 0.2426 REMARK 3 T33: 0.4906 T12: -0.0164 REMARK 3 T13: 0.0044 T23: 0.0566 REMARK 3 L TENSOR REMARK 3 L11: 3.5887 L22: 1.6491 REMARK 3 L33: 1.0222 L12: -0.0984 REMARK 3 L13: 1.0122 L23: 0.3996 REMARK 3 S TENSOR REMARK 3 S11: 0.1311 S12: 0.0845 S13: -0.5387 REMARK 3 S21: -0.0148 S22: -0.0911 S23: -0.1374 REMARK 3 S31: -0.0015 S32: 0.1799 S33: -0.0365 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -3.6693 -21.7585 19.2319 REMARK 3 T TENSOR REMARK 3 T11: 0.4686 T22: 0.4434 REMARK 3 T33: 0.4411 T12: -0.0992 REMARK 3 T13: -0.1569 T23: 0.0754 REMARK 3 L TENSOR REMARK 3 L11: 1.9476 L22: 0.2894 REMARK 3 L33: 2.6361 L12: 1.0370 REMARK 3 L13: 1.5839 L23: -1.1876 REMARK 3 S TENSOR REMARK 3 S11: -0.4447 S12: 0.5603 S13: 0.3565 REMARK 3 S21: -0.2966 S22: 0.3693 S23: 0.6780 REMARK 3 S31: -0.0478 S32: -0.0211 S33: 0.0347 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 17.6345 -15.8317 22.1585 REMARK 3 T TENSOR REMARK 3 T11: 0.5045 T22: 0.7139 REMARK 3 T33: 0.4006 T12: -0.2676 REMARK 3 T13: -0.0006 T23: 0.0536 REMARK 3 L TENSOR REMARK 3 L11: 7.5850 L22: 1.9854 REMARK 3 L33: 4.6910 L12: 2.2468 REMARK 3 L13: 4.6353 L23: 2.8728 REMARK 3 S TENSOR REMARK 3 S11: -0.5118 S12: 1.1679 S13: -0.6497 REMARK 3 S21: -0.5392 S22: 0.9323 S23: -0.2906 REMARK 3 S31: -0.8168 S32: 1.1752 S33: -0.3127 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 15.9406 -18.6919 18.9447 REMARK 3 T TENSOR REMARK 3 T11: 0.5076 T22: 1.1789 REMARK 3 T33: 0.3641 T12: -0.1472 REMARK 3 T13: -0.0191 T23: -0.2412 REMARK 3 L TENSOR REMARK 3 L11: 3.4156 L22: 2.8313 REMARK 3 L33: 3.3687 L12: 4.1483 REMARK 3 L13: 4.8640 L23: 2.3818 REMARK 3 S TENSOR REMARK 3 S11: -0.7151 S12: 1.9328 S13: -0.6755 REMARK 3 S21: -0.6602 S22: 0.8596 S23: -0.2325 REMARK 3 S31: -1.0326 S32: 1.6318 S33: -0.1043 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3G6U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051496. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-07 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27530 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 72.6 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.46600 REMARK 200 R SYM FOR SHELL (I) : 0.80700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1GLU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES, PH 7.5, 2.5MM SPERMINE, REMARK 280 80MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 58.12150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.54400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.12150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.54400 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C 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 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 436 REMARK 465 LYS A 514 REMARK 465 LYS A 515 REMARK 465 ILE A 516 REMARK 465 LYS A 517 REMARK 465 GLY A 518 REMARK 465 ILE A 519 REMARK 465 GLN A 520 REMARK 465 GLN A 521 REMARK 465 ALA A 522 REMARK 465 THR A 523 REMARK 465 ALA A 524 REMARK 465 GLY A 525 REMARK 465 GLY B 436 REMARK 465 LYS B 513 REMARK 465 LYS B 514 REMARK 465 LYS B 515 REMARK 465 ILE B 516 REMARK 465 LYS B 517 REMARK 465 GLY B 518 REMARK 465 ILE B 519 REMARK 465 GLN B 520 REMARK 465 GLN B 521 REMARK 465 ALA B 522 REMARK 465 THR B 523 REMARK 465 ALA B 524 REMARK 465 GLY B 525 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 SER A 437 OG REMARK 470 LYS A 513 CG CD CE NZ REMARK 470 SER B 437 OG REMARK 470 LYS B 511 CG CD CE NZ REMARK 470 THR B 512 OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OP1 DT D 16 O5' DA C 1 2656 2.15 REMARK 500 O HOH C 80 O HOH C 80 2656 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 442 CB VAL A 442 CG1 0.142 REMARK 500 DG D 8 O3' DG D 8 C3' -0.045 REMARK 500 DG D 12 P DG D 12 O5' 0.072 REMARK 500 DG D 12 C5' DG D 12 C4' 0.043 REMARK 500 DT D 13 O3' DT D 13 C3' -0.048 REMARK 500 DC D 15 O3' DC D 15 C3' -0.043 REMARK 500 DA C 1 C5 DA C 1 C6 -0.054 REMARK 500 DA C 1 N9 DA C 1 C4 -0.065 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 ARG B 479 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 DG D 3 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DG D 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA D 7 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA D 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 11 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG D 12 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DG D 12 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DG D 12 C3' - C2' - C1' ANGL. DEV. = -7.3 DEGREES REMARK 500 DT D 13 O3' - P - OP2 ANGL. DEV. = 11.5 DEGREES REMARK 500 DT D 13 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT D 14 O3' - P - OP2 ANGL. DEV. = 7.9 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = -9.1 DEGREES REMARK 500 DT D 14 N3 - C4 - O4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT D 14 C5 - C4 - O4 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC D 15 O5' - P - OP2 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT D 16 O5' - C5' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DA C 1 C5' - C4' - C3' ANGL. DEV. = -15.4 DEGREES REMARK 500 DA C 1 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 DA C 1 O4' - C1' - C2' ANGL. DEV. = 5.0 DEGREES REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA C 1 C6 - N1 - C2 ANGL. DEV. = 5.2 DEGREES REMARK 500 DA C 1 C2 - N3 - C4 ANGL. DEV. = -8.3 DEGREES REMARK 500 DA C 1 N3 - C4 - C5 ANGL. DEV. = 8.1 DEGREES REMARK 500 DA C 1 C5 - C6 - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA C 1 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA C 1 N3 - C4 - N9 ANGL. DEV. = -7.3 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA C 2 C6 - N1 - C2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA C 2 C5 - C6 - N6 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG C 3 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA C 4 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DA C 5 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT C 11 N3 - C4 - O4 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT C 11 C5 - C4 - O4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT C 14 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT C 14 C6 - C5 - C7 ANGL. DEV. = -3.9 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 HIS A 438 37.70 -146.20 REMARK 500 HIS A 472 46.48 -148.18 REMARK 500 HIS A 472 53.86 -148.18 REMARK 500 ASN A 473 24.39 -70.39 REMARK 500 ASP A 481 38.71 -143.35 REMARK 500 THR A 512 49.93 -96.27 REMARK 500 HIS B 438 -86.53 -114.11 REMARK 500 MET B 439 127.91 -172.74 REMARK 500 ASP B 445 -161.25 -72.58 REMARK 500 ASP B 481 37.96 -145.57 REMARK 500 ASP B 481 44.43 -156.12 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 ZN A 526 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 440 SG REMARK 620 2 CYS A 443 SG 110.9 REMARK 620 3 CYS A 457 SG 112.3 109.0 REMARK 620 4 CYS A 460 SG 110.5 110.3 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 527 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 476 SG REMARK 620 2 CYS A 482 SG 104.8 REMARK 620 3 CYS A 492 SG 114.4 115.0 REMARK 620 4 CYS A 495 SG 107.3 107.4 107.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 526 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 440 SG REMARK 620 2 CYS B 443 SG 120.1 REMARK 620 3 CYS B 457 SG 115.7 104.0 REMARK 620 4 CYS B 460 SG 106.9 113.3 93.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 527 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 476 SG REMARK 620 2 CYS B 482 SG 105.0 REMARK 620 3 CYS B 492 SG 114.0 112.7 REMARK 620 4 CYS B 495 SG 107.5 110.9 106.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 527 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FYL RELATED DB: PDB REMARK 900 SAME PROTEIN, DIFFERENT DNA REMARK 900 RELATED ID: 3G6P RELATED DB: PDB REMARK 900 SAME COMPLEX, DIFFERENT CRYSTAL CONDITION REMARK 900 RELATED ID: 3G6Q RELATED DB: PDB REMARK 900 SAME DNA BINDING SITE, INSERTION MUTATION GR GAMMA REMARK 900 RELATED ID: 3G6R RELATED DB: PDB REMARK 900 RELATED ID: 3G6T RELATED DB: PDB REMARK 900 RELATED ID: 3G8X RELATED DB: PDB REMARK 900 RELATED ID: 3G97 RELATED DB: PDB REMARK 900 RELATED ID: 3G99 RELATED DB: PDB DBREF 3G6U A 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G6U B 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G6U C 1 16 PDB 3G6U 3G6U 1 16 DBREF 3G6U D 1 16 PDB 3G6U 3G6U 1 16 SEQADV 3G6U GLY A 436 UNP P06536 EXPRESSION TAG SEQADV 3G6U SER A 437 UNP P06536 EXPRESSION TAG SEQADV 3G6U HIS A 438 UNP P06536 EXPRESSION TAG SEQADV 3G6U MET A 439 UNP P06536 EXPRESSION TAG SEQADV 3G6U GLY B 436 UNP P06536 EXPRESSION TAG SEQADV 3G6U SER B 437 UNP P06536 EXPRESSION TAG SEQADV 3G6U HIS B 438 UNP P06536 EXPRESSION TAG SEQADV 3G6U MET B 439 UNP P06536 EXPRESSION TAG SEQRES 1 A 90 GLY SER HIS MET CYS LEU VAL CYS SER ASP GLU ALA SER SEQRES 2 A 90 GLY CYS HIS TYR GLY VAL LEU THR CYS GLY SER CYS LYS SEQRES 3 A 90 VAL PHE PHE LYS ARG ALA VAL GLU GLY GLN HIS ASN TYR SEQRES 4 A 90 LEU CYS ALA GLY ARG ASN ASP CYS ILE ILE ASP LYS ILE SEQRES 5 A 90 ARG ARG LYS ASN CYS PRO ALA CYS ARG TYR ARG LYS CYS SEQRES 6 A 90 LEU GLN ALA GLY MET ASN LEU GLU ALA ARG LYS THR LYS SEQRES 7 A 90 LYS LYS ILE LYS GLY ILE GLN GLN ALA THR ALA GLY SEQRES 1 B 90 GLY SER HIS MET CYS LEU VAL CYS SER ASP GLU ALA SER SEQRES 2 B 90 GLY CYS HIS TYR GLY VAL LEU THR CYS GLY SER CYS LYS SEQRES 3 B 90 VAL PHE PHE LYS ARG ALA VAL GLU GLY GLN HIS ASN TYR SEQRES 4 B 90 LEU CYS ALA GLY ARG ASN ASP CYS ILE ILE ASP LYS ILE SEQRES 5 B 90 ARG ARG LYS ASN CYS PRO ALA CYS ARG TYR ARG LYS CYS SEQRES 6 B 90 LEU GLN ALA GLY MET ASN LEU GLU ALA ARG LYS THR LYS SEQRES 7 B 90 LYS LYS ILE LYS GLY ILE GLN GLN ALA THR ALA GLY SEQRES 1 D 16 DT DA DG DA DA DC DA DG DG DG DT DG DT SEQRES 2 D 16 DT DC DT SEQRES 1 C 16 DA DA DG DA DA DC DA DC DC DC DT DG DT SEQRES 2 C 16 DT DC DT HET ZN A 526 1 HET ZN A 527 1 HET ZN B 526 1 HET ZN B 527 1 HETNAM ZN ZINC ION FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *83(H2 O) HELIX 1 1 CYS A 457 GLY A 470 1 14 HELIX 2 2 CYS A 492 GLY A 504 1 13 HELIX 3 3 ASN A 506 ARG A 510 5 5 HELIX 4 4 CYS B 457 GLN B 471 1 15 HELIX 5 5 CYS B 492 ALA B 503 1 12 HELIX 6 6 ASN B 506 ARG B 510 5 5 SHEET 1 A 2 GLY A 449 HIS A 451 0 SHEET 2 A 2 VAL A 454 THR A 456 -1 O VAL A 454 N HIS A 451 SHEET 1 B 2 CYS B 450 HIS B 451 0 SHEET 2 B 2 VAL B 454 LEU B 455 -1 O VAL B 454 N HIS B 451 LINK SG CYS A 440 ZN ZN A 526 1555 1555 2.23 LINK SG CYS A 443 ZN ZN A 526 1555 1555 2.30 LINK SG CYS A 457 ZN ZN A 526 1555 1555 2.29 LINK SG CYS A 460 ZN ZN A 526 1555 1555 2.31 LINK SG CYS A 476 ZN ZN A 527 1555 1555 2.32 LINK SG CYS A 482 ZN ZN A 527 1555 1555 2.34 LINK SG CYS A 492 ZN ZN A 527 1555 1555 2.34 LINK SG CYS A 495 ZN ZN A 527 1555 1555 2.33 LINK SG CYS B 440 ZN ZN B 526 1555 1555 2.29 LINK SG CYS B 443 ZN ZN B 526 1555 1555 2.31 LINK SG CYS B 457 ZN ZN B 526 1555 1555 2.38 LINK SG CYS B 460 ZN ZN B 526 1555 1555 2.35 LINK SG CYS B 476 ZN ZN B 527 1555 1555 2.27 LINK SG CYS B 482 ZN ZN B 527 1555 1555 2.30 LINK SG CYS B 492 ZN ZN B 527 1555 1555 2.34 LINK SG CYS B 495 ZN ZN B 527 1555 1555 2.38 SITE 1 AC1 4 CYS A 440 CYS A 443 CYS A 457 CYS A 460 SITE 1 AC2 4 CYS A 476 CYS A 482 CYS A 492 CYS A 495 SITE 1 AC3 4 CYS B 440 CYS B 443 CYS B 457 CYS B 460 SITE 1 AC4 4 CYS B 476 CYS B 482 CYS B 492 CYS B 495 CRYST1 116.243 39.088 95.610 90.00 122.67 90.00 C 1 2 1 8 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 0.008603 0.000000 0.005516 0.00000 SCALE2 0.000000 0.025583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012425 0.00000