PDB Short entry for 3G9I HEADER TRANSCRIPTION/DNA 13-FEB-09 3G9I TITLE GR DNA BINDING DOMAIN: PAL COMPLEX-35 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*AP*AP*AP*TP*GP*TP*TP*CP*T)- COMPND 9 3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: GR BINDING SITE: PAL BOTTOM STRAND; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*T)- COMPND 15 3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: GR BINDING SITE: PAL 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 3G9I 1 REMARK SEQADV REVDAT 3 01-NOV-17 3G9I 1 REMARK REVDAT 2 02-JUN-09 3G9I 1 JRNL REVDAT 1 21-APR-09 3G9I 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.200 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.7 REMARK 3 NUMBER OF REFLECTIONS : 24291 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.570 REMARK 3 FREE R VALUE TEST SET COUNT : 1838 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 48.8306 - 3.9852 0.99 2866 232 0.1518 0.1639 REMARK 3 2 3.9852 - 3.1634 0.97 2726 222 0.1542 0.1923 REMARK 3 3 3.1634 - 2.7635 0.96 2687 222 0.1847 0.2073 REMARK 3 4 2.7635 - 2.5109 0.94 2591 223 0.1608 0.2100 REMARK 3 5 2.5109 - 2.3309 0.90 2499 192 0.1577 0.2322 REMARK 3 6 2.3309 - 2.1935 0.87 2428 195 0.1728 0.1938 REMARK 3 7 2.1935 - 2.0836 0.83 2265 192 0.1897 0.2505 REMARK 3 8 2.0836 - 1.9929 0.68 1884 151 0.2158 0.2404 REMARK 3 9 1.9929 - 1.9162 0.54 1486 124 0.2411 0.2547 REMARK 3 10 1.9162 - 1.8500 0.37 1021 85 0.2817 0.3681 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 : 0.40 REMARK 3 B_SOL : 70.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.830 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.51 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 : 0.011 NULL REMARK 3 ANGLE : NULL 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): -35.7216 11.6054 -21.9032 REMARK 3 T TENSOR REMARK 3 T11: 0.4476 T22: 0.5012 REMARK 3 T33: 0.2313 T12: -0.0642 REMARK 3 T13: -0.0395 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 2.0007 L22: 1.7045 REMARK 3 L33: -1.3214 L12: 0.4552 REMARK 3 L13: -0.7316 L23: -0.2947 REMARK 3 S TENSOR REMARK 3 S11: -0.2506 S12: 0.8637 S13: -0.0448 REMARK 3 S21: -0.5721 S22: 0.2064 S23: 0.1863 REMARK 3 S31: 0.1285 S32: -0.3338 S33: 0.0125 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -19.0526 16.5010 1.2088 REMARK 3 T TENSOR REMARK 3 T11: 0.1915 T22: 0.1427 REMARK 3 T33: 0.2892 T12: -0.0104 REMARK 3 T13: 0.0114 T23: 0.0322 REMARK 3 L TENSOR REMARK 3 L11: 1.8872 L22: 1.6669 REMARK 3 L33: 1.1345 L12: -0.6967 REMARK 3 L13: 0.3440 L23: 0.6765 REMARK 3 S TENSOR REMARK 3 S11: 0.1034 S12: 0.0154 S13: -0.2626 REMARK 3 S21: -0.0389 S22: -0.0496 S23: -0.2003 REMARK 3 S31: 0.0565 S32: 0.2090 S33: -0.0551 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -16.3757 14.6167 -21.6536 REMARK 3 T TENSOR REMARK 3 T11: 0.2892 T22: 0.7872 REMARK 3 T33: 0.2859 T12: -0.0680 REMARK 3 T13: 0.0697 T23: -0.1847 REMARK 3 L TENSOR REMARK 3 L11: -0.1140 L22: 2.0692 REMARK 3 L33: 3.6083 L12: 2.7451 REMARK 3 L13: 2.1657 L23: 1.7153 REMARK 3 S TENSOR REMARK 3 S11: -0.3219 S12: 1.1946 S13: -0.5977 REMARK 3 S21: -0.3225 S22: 0.6136 S23: -0.3096 REMARK 3 S31: -0.6770 S32: 1.0644 S33: -0.2614 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): -14.3533 17.5282 -17.8073 REMARK 3 T TENSOR REMARK 3 T11: 0.3740 T22: 0.5203 REMARK 3 T33: 0.2513 T12: -0.1436 REMARK 3 T13: 0.0813 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 3.0318 L22: 1.9107 REMARK 3 L33: 3.4756 L12: 1.3257 REMARK 3 L13: -0.0320 L23: 1.9347 REMARK 3 S TENSOR REMARK 3 S11: -0.2155 S12: 0.8480 S13: -0.6085 REMARK 3 S21: -0.4973 S22: 0.6170 S23: -0.2561 REMARK 3 S31: -0.6718 S32: 0.8439 S33: -0.3095 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 3G9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.115879 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) 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 : 26375 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.04700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.62800 REMARK 200 R SYM FOR SHELL (I) : 0.56900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 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: 1GLU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES, PH 7.0, 100MM KCL, 10MM REMARK 280 MGCL2, 5% PEG400, 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 58.25650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.82400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.25650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.82400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 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 350 REMARK 350 BIOMOLECULE: 2 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: 5400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 68 LIES ON A SPECIAL POSITION. 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 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 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 LYS A 514 CG CD CE NZ REMARK 470 LYS A 515 CG CD CE NZ REMARK 470 SER B 437 OG REMARK 470 LYS B 511 CG CD CE NZ REMARK 470 LYS B 514 CG CD CE NZ REMARK 470 LYS B 515 CG CD CE NZ REMARK 470 ILE B 516 CG1 CG2 CD1 REMARK 470 LYS B 517 CG CD CE NZ 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 O1 EDO A 2 O HOH A 140 2.12 REMARK 500 OP1 DT C 16 O HOH C 85 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 O1 EDO A 3 O2 EDO B 1 4445 1.86 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 DG D 3 O3' DG D 3 C3' -0.059 REMARK 500 DG C 3 O3' DG C 3 C3' -0.041 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 DA D 2 O5' - C5' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 DG D 3 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA D 8 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA D 8 N1 - C6 - N6 ANGL. DEV. = 5.6 DEGREES REMARK 500 DA D 8 C5 - C6 - N6 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA D 9 O4' - C1' - N9 ANGL. DEV. = -9.3 DEGREES REMARK 500 DA D 9 C4 - C5 - N7 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA D 9 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA D 9 N1 - C6 - N6 ANGL. DEV. = 6.8 DEGREES REMARK 500 DA D 9 C5 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT D 13 O4' - C1' - N1 ANGL. DEV. = -7.6 DEGREES REMARK 500 DA C 1 O4' - C1' - C2' ANGL. DEV. = 4.0 DEGREES REMARK 500 DA C 1 N1 - C2 - N3 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA C 1 C2 - N3 - C4 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT C 8 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT C 9 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DT C 10 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG C 12 C5 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT C 14 O3' - P - OP2 ANGL. DEV. = 7.5 DEGREES REMARK 500 DT C 14 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC C 15 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DT C 16 O4' - C4' - C3' ANGL. DEV. = -2.5 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 GLN A 471 29.53 43.45 REMARK 500 ARG A 479 22.58 -140.92 REMARK 500 ASP A 481 38.69 -145.30 REMARK 500 GLU A 508 51.61 -106.63 REMARK 500 HIS B 438 18.26 -163.85 REMARK 500 HIS B 472 49.85 -141.91 REMARK 500 ASP B 481 40.00 -142.13 REMARK 500 ASP B 485 -169.99 -123.83 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 108.2 REMARK 620 3 CYS A 457 SG 116.5 106.2 REMARK 620 4 CYS A 460 SG 111.2 111.6 103.1 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 102.6 REMARK 620 3 CYS A 492 SG 114.3 113.2 REMARK 620 4 CYS A 495 SG 109.8 110.8 106.2 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 110.2 REMARK 620 3 CYS B 457 SG 114.6 106.9 REMARK 620 4 CYS B 460 SG 109.7 112.1 103.2 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 102.3 REMARK 620 3 CYS B 492 SG 110.9 116.0 REMARK 620 4 CYS B 495 SG 110.3 110.5 106.8 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 EDO A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1 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: 3G6U RELATED DB: PDB REMARK 900 RELATED ID: 3G8U 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 REMARK 900 RELATED ID: 3G9J RELATED DB: PDB REMARK 900 RELATED ID: 3G9M RELATED DB: PDB REMARK 900 RELATED ID: 3G9O RELATED DB: PDB REMARK 900 RELATED ID: 3G9P RELATED DB: PDB DBREF 3G9I A 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G9I B 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G9I C 1 16 PDB 3G9I 3G9I 1 16 DBREF 3G9I D 1 16 PDB 3G9I 3G9I 1 16 SEQADV 3G9I GLY A 436 UNP P06536 EXPRESSION TAG SEQADV 3G9I SER A 437 UNP P06536 EXPRESSION TAG SEQADV 3G9I HIS A 438 UNP P06536 EXPRESSION TAG SEQADV 3G9I MET A 439 UNP P06536 EXPRESSION TAG SEQADV 3G9I GLY B 436 UNP P06536 EXPRESSION TAG SEQADV 3G9I SER B 437 UNP P06536 EXPRESSION TAG SEQADV 3G9I HIS B 438 UNP P06536 EXPRESSION TAG SEQADV 3G9I 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 DA DA DA DT DG DT SEQRES 2 D 16 DT DC DT SEQRES 1 C 16 DA DA DG DA DA DC DA DT DT DT DT DG DT SEQRES 2 C 16 DT DC DT HET ZN A 526 1 HET ZN A 527 1 HET EDO A 2 4 HET EDO A 3 4 HET ZN B 526 1 HET ZN B 527 1 HET EDO B 1 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 ZN 4(ZN 2+) FORMUL 7 EDO 3(C2 H6 O2) FORMUL 12 HOH *164(H2 O) HELIX 1 1 CYS A 457 GLY A 470 1 14 HELIX 2 2 ILE A 487 ASN A 491 5 5 HELIX 3 3 CYS A 492 ALA A 503 1 12 HELIX 4 4 CYS B 457 GLY B 470 1 14 HELIX 5 5 ILE B 487 ASN B 491 5 5 HELIX 6 6 CYS B 492 GLY B 504 1 13 HELIX 7 7 GLU B 508 ILE B 516 1 9 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 GLY B 449 HIS B 451 0 SHEET 2 B 2 VAL B 454 THR B 456 -1 O VAL B 454 N HIS B 451 LINK SG CYS A 440 ZN ZN A 526 1555 1555 2.35 LINK SG CYS A 443 ZN ZN A 526 1555 1555 2.23 LINK SG CYS A 457 ZN ZN A 526 1555 1555 2.31 LINK SG CYS A 460 ZN ZN A 526 1555 1555 2.33 LINK SG CYS A 476 ZN ZN A 527 1555 1555 2.23 LINK SG CYS A 482 ZN ZN A 527 1555 1555 2.28 LINK SG CYS A 492 ZN ZN A 527 1555 1555 2.37 LINK SG CYS A 495 ZN ZN A 527 1555 1555 2.36 LINK SG CYS B 440 ZN ZN B 526 1555 1555 2.36 LINK SG CYS B 443 ZN ZN B 526 1555 1555 2.31 LINK SG CYS B 457 ZN ZN B 526 1555 1555 2.34 LINK SG CYS B 460 ZN ZN B 526 1555 1555 2.28 LINK SG CYS B 476 ZN ZN B 527 1555 1555 2.32 LINK SG CYS B 482 ZN ZN B 527 1555 1555 2.20 LINK SG CYS B 492 ZN ZN B 527 1555 1555 2.39 LINK SG CYS B 495 ZN ZN B 527 1555 1555 2.34 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 3 HOH A 140 HOH A 143 ALA A 494 SITE 1 AC4 5 HOH A 127 ARG A 479 EDO B 1 GLY B 470 SITE 2 AC4 5 ARG B 479 SITE 1 AC5 4 CYS B 440 CYS B 443 CYS B 457 CYS B 460 SITE 1 AC6 4 CYS B 476 CYS B 482 CYS B 492 CYS B 495 SITE 1 AC7 3 EDO A 3 GLU B 469 GLN B 471 CRYST1 116.513 37.648 95.448 90.00 123.08 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 0.008583 0.000000 0.005591 0.00000 SCALE2 0.000000 0.026562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012504 0.00000