10 20 30 40 50 60 70 80 3G99 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER TRANSCRIPTION/DNA 13-FEB-09 3G99
TITLE GR DNA BINDING DOMAIN:PAL COMPLEX-9
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'- COMPND 9 D(*TP*AP*GP*AP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: GLUCOCORTICOID RECEPTOR BINDING SITE PAL COMPND 13 BOTTOM STRAND; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'- COMPND 16 D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*T)-3'); COMPND 17 CHAIN: C; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: GLUCOCORTICOID RECEPTOR BINDING SITE PAL TOP COMPND 20 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, KEYWDS 2 TRANSCRIPTION, HORMONE, ALTERNATIVE INITIATION, CHROMATIN KEYWDS 3 REGULATOR, CYTOPLASM, LIPID-BINDING, METAL-BINDING, KEYWDS 4 NUCLEUS, PHOSPHOPROTEIN, POLYMORPHISM, RECEPTOR, STEROID- KEYWDS 5 BINDING, TRANSCRIPTION REGULATION, UBL CONJUGATION, ZINC, KEYWDS 6 ZINC-FINGER, TRANSCRIPTION/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.A.PUFALL,K.R.YAMAMOTO,S.H.MEIJSING
REVDAT 2 02-JUN-09 3G99 1 JRNL REVDAT 1 21-APR-09 3G99 0
JRNL AUTH S.H.MEIJSING,M.A.PUFALL,A.Y.SO,D.L.BATES,L.CHEN, JRNL AUTH 2 K.R.YAMAMOTO JRNL TITL DNA BINDING SITE SEQUENCE DIRECTS GLUCOCORTICOID JRNL TITL 2 RECEPTOR 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 1
REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 66.4 REMARK 3 NUMBER OF REFLECTIONS : 22269 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.270 REMARK 3 FREE R VALUE TEST SET COUNT : 1842 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 35.5807 - 3.8832 0.99 3165 279 0.1514 0.1904 REMARK 3 2 3.8832 - 3.0827 0.97 3026 275 0.1952 0.2349 REMARK 3 3 3.0827 - 2.6932 0.93 2878 252 0.2294 0.2452 REMARK 3 4 2.6932 - 2.4470 0.89 2738 249 0.2092 0.2559 REMARK 3 5 2.4470 - 2.2717 0.85 2582 233 0.2008 0.2446 REMARK 3 6 2.2717 - 2.1378 0.74 2268 200 0.2271 0.2719 REMARK 3 7 2.1378 - 2.0307 0.58 1759 164 0.2481 0.3352 REMARK 3 8 2.0307 - 1.9423 0.38 1168 106 0.2856 0.3457 REMARK 3 9 1.9423 - 1.8676 0.20 604 62 0.2904 0.3481 REMARK 3 10 1.8676 - 1.8100 0.08 239 22 0.2981 0.3712 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 : 0.38 REMARK 3 B_SOL : 64.12 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.730 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.00 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 : 0.014 NULL REMARK 3 ANGLE : 1.528 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): 12.4580 -15.8029 41.4089 REMARK 3 T TENSOR REMARK 3 T11: 0.1831 T22: 0.1653 REMARK 3 T33: 0.3266 T12: -0.0134 REMARK 3 T13: 0.0215 T23: 0.0760 REMARK 3 L TENSOR REMARK 3 L11: 2.4714 L22: 1.8171 REMARK 3 L33: 1.4607 L12: -0.2190 REMARK 3 L13: 0.2559 L23: 0.4277 REMARK 3 S TENSOR REMARK 3 S11: 0.1434 S12: 0.0029 S13: -0.4807 REMARK 3 S21: -0.0992 S22: -0.1502 S23: -0.2852 REMARK 3 S31: -0.0547 S32: 0.1561 S33: 0.0018 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -3.5777 -20.3339 20.0392 REMARK 3 T TENSOR REMARK 3 T11: 0.3846 T22: 0.2426 REMARK 3 T33: 0.2333 T12: 0.0027 REMARK 3 T13: -0.1066 T23: -0.0481 REMARK 3 L TENSOR REMARK 3 L11: 2.2062 L22: 0.9058 REMARK 3 L33: 0.4740 L12: 0.6958 REMARK 3 L13: 0.0119 L23: -0.1874 REMARK 3 S TENSOR REMARK 3 S11: -0.2420 S12: 0.4577 S13: 0.0417 REMARK 3 S21: -0.3521 S22: 0.0326 S23: 0.3059 REMARK 3 S31: -0.0304 S32: 0.0779 S33: 0.0644 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 17.3973 -14.9492 22.9338 REMARK 3 T TENSOR REMARK 3 T11: 0.5451 T22: 0.5179 REMARK 3 T33: 0.3756 T12: -0.1953 REMARK 3 T13: 0.1027 T23: 0.0349 REMARK 3 L TENSOR REMARK 3 L11: 2.9037 L22: 2.1192 REMARK 3 L33: 2.4654 L12: 1.4951 REMARK 3 L13: -0.5955 L23: 2.5323 REMARK 3 S TENSOR REMARK 3 S11: -0.3744 S12: 0.8744 S13: -0.5686 REMARK 3 S21: -0.7222 S22: 0.8346 S23: -0.2764 REMARK 3 S31: -0.9568 S32: 0.6457 S33: -0.3075 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 15.2612 -17.7525 18.9426 REMARK 3 T TENSOR REMARK 3 T11: 0.4866 T22: 0.8420 REMARK 3 T33: 0.3066 T12: -0.1222 REMARK 3 T13: 0.1204 T23: -0.1595 REMARK 3 L TENSOR REMARK 3 L11: -0.2119 L22: 2.7611 REMARK 3 L33: 2.3009 L12: 1.4471 REMARK 3 L13: 1.2262 L23: 1.6048 REMARK 3 S TENSOR REMARK 3 S11: -0.4556 S12: 1.1495 S13: -0.5167 REMARK 3 S21: -0.7601 S22: 0.5732 S23: -0.4933 REMARK 3 S31: -0.6564 S32: 0.8053 S33: -0.1918 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 3G99 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-09. REMARK 100 THE RCSB ID CODE IS RCSB051583.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 1.115894 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 : 24846 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 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 (%) : 73.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.05200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 10.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.63300 REMARK 200 R SYM FOR SHELL (I) : 0.48900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 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 (%): 59.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES, PH 6.0, 100 KCL, 10MM REMARK 280 MGCL2, 10% PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 58.38700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.09450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.38700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.09450 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: 6050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 SER B 437 REMARK 465 LYS B 511 REMARK 465 THR B 512 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 LYS A 514 CG CD CE NZ REMARK 470 LYS A 515 CG CD CE NZ REMARK 470 ARG B 510 CG CD NE CZ NH1 NH2 REMARK 470 DT C 8 C7
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 C2 DA C 1 N1 DA C 2 2656 2.18 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 468 CB VAL A 468 CG2 -0.133 REMARK 500 DA D 10 O3' DA D 10 C3' -0.048 REMARK 500 DG D 12 O3' DG D 12 C3' -0.043 REMARK 500 DT D 13 O3' DT D 13 C3' -0.040 REMARK 500 DC D 15 O3' DC D 15 C3' -0.039 REMARK 500 DG C 3 C5 DG C 3 N7 0.041 REMARK 500 DT C 9 O3' DT C 9 C3' -0.043 REMARK 500 DT C 10 O3' DT C 10 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 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA D 9 O4' - C1' - N9 ANGL. DEV. = -10.5 DEGREES REMARK 500 DA D 10 O5' - C5' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DA D 10 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DG D 12 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT D 14 O5' - C5' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 DT D 14 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DC D 15 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DC D 15 C1' - O4' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = -6.3 DEGREES REMARK 500 DC D 15 C6 - N1 - C2 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT D 14 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DT D 16 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT D 16 N3 - C4 - O4 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA C 1 N9 - C1' - C2' ANGL. DEV. = -13.8 DEGREES REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = -6.8 DEGREES REMARK 500 DA C 1 C6 - N1 - C2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA C 1 N1 - C2 - N3 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA C 1 C2 - N3 - C4 ANGL. DEV. = -8.0 DEGREES REMARK 500 DA C 1 N3 - C4 - C5 ANGL. DEV. = 6.0 DEGREES REMARK 500 DA C 1 C5 - C6 - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA C 1 N3 - C4 - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA C 2 O5' - C5' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DA C 2 C4 - C5 - C6 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG C 3 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 2 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DT C 8 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT C 8 C4 - C5 - C6 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT C 8 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT C 8 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT C 9 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT C 11 N3 - C4 - O4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG C 12 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = -8.3 DEGREES REMARK 500 DT C 13 C6 - N1 - C2 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC C 15 C3' - C2' - C1' ANGL. DEV. = -7.7 DEGREES REMARK 500 DT C 16 O4' - C4' - C3' ANGL. DEV. = -4.1 DEGREES REMARK 500 DT C 16 C4' - C3' - C2' ANGL. DEV. = -5.0 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 25.98 -142.99 REMARK 500 ASP A 481 38.48 -151.09 REMARK 500 GLU A 508 45.57 -100.71 REMARK 500 ASP B 445 -161.23 -69.22 REMARK 500 TYR B 452 32.82 38.41 REMARK 500 LEU B 455 97.78 -65.38 REMARK 500 ARG B 479 19.40 -145.07 REMARK 500 ASP B 481 44.67 -148.15 REMARK 500 ALA B 509 -52.74 -137.46 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 111.3 REMARK 620 3 CYS A 457 SG 114.3 107.4 REMARK 620 4 CYS A 460 SG 107.7 111.7 104.2 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 102.3 REMARK 620 3 CYS A 492 SG 109.8 115.8 REMARK 620 4 CYS A 495 SG 111.7 108.6 108.6 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 110.7 REMARK 620 3 CYS B 457 SG 112.1 110.1 REMARK 620 4 CYS B 460 SG 109.4 115.7 98.3 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 107.0 REMARK 620 3 CYS B 492 SG 110.9 116.2 REMARK 620 4 CYS B 495 SG 106.1 111.4 104.8 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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 527 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 526 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 527 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 17 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR C 17
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: 3G6U RELATED DB: PDB REMARK 900 RELATED ID: 3G8X RELATED DB: PDB REMARK 900 RELATED ID: 3G97 RELATED DB: PDB REMARK 900 RELATED ID: 3G9I 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 3G99 A 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G99 B 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G99 C 1 16 PDB 3G99 3G99 1 16 DBREF 3G99 D 1 16 PDB 3G99 3G99 1 16
SEQADV 3G99 GLY A 436 UNP P06536 EXPRESSION TAG SEQADV 3G99 SER A 437 UNP P06536 EXPRESSION TAG SEQADV 3G99 HIS A 438 UNP P06536 EXPRESSION TAG SEQADV 3G99 MET A 439 UNP P06536 EXPRESSION TAG SEQADV 3G99 GLY B 436 UNP P06536 EXPRESSION TAG SEQADV 3G99 SER B 437 UNP P06536 EXPRESSION TAG SEQADV 3G99 HIS B 438 UNP P06536 EXPRESSION TAG SEQADV 3G99 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 1 4 HET ZN B 526 1 HET ZN B 527 1 HET EDO D 17 4 HET BR C 17 1
HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM BR BROMIDE ION
HETSYN EDO ETHYLENE GLYCOL
FORMUL 5 ZN 4(ZN 2+) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 11 BR BR 1- FORMUL 12 HOH *94(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 GLY A 504 1 13 HELIX 4 4 GLU A 508 LYS A 514 1 7 HELIX 5 5 CYS B 457 GLY B 470 1 14 HELIX 6 6 ILE B 487 ASN B 491 5 5 HELIX 7 7 CYS B 492 ALA B 503 1 12
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 2.45 LINK SG CYS A 443 ZN ZN A 526 1555 1555 2.31 LINK SG CYS A 457 ZN ZN A 526 1555 1555 2.33 LINK SG CYS A 460 ZN ZN A 526 1555 1555 2.20 LINK SG CYS A 476 ZN ZN A 527 1555 1555 2.29 LINK SG CYS A 482 ZN ZN A 527 1555 1555 2.20 LINK SG CYS A 492 ZN ZN A 527 1555 1555 2.42 LINK SG CYS A 495 ZN ZN A 527 1555 1555 2.34 LINK SG CYS B 440 ZN ZN B 526 1555 1555 2.34 LINK SG CYS B 443 ZN ZN B 526 1555 1555 2.32 LINK SG CYS B 457 ZN ZN B 526 1555 1555 2.23 LINK SG CYS B 460 ZN ZN B 526 1555 1555 2.24 LINK SG CYS B 476 ZN ZN B 527 1555 1555 2.20 LINK SG CYS B 482 ZN ZN B 527 1555 1555 2.22 LINK SG CYS B 492 ZN ZN B 527 1555 1555 2.37 LINK SG CYS B 495 ZN ZN B 527 1555 1555 2.48
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 7 HOH A 95 LYS A 490 ASN A 491 LYS B 490 SITE 2 AC3 7 DT C 11 DA D 10 DT D 11 SITE 1 AC4 4 CYS B 440 CYS B 443 CYS B 457 CYS B 460 SITE 1 AC5 4 CYS B 476 CYS B 482 CYS B 492 CYS B 495 SITE 1 AC6 6 PHE A 463 ARG A 466 DT D 11 HOH D 22 SITE 2 AC6 6 HOH D 59 HOH D 70 SITE 1 AC7 2 DA C 7 DT C 8
CRYST1 116.774 38.189 97.064 90.00 123.11 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 0.008564 0.000000 0.005585 0.00000
SCALE2 0.000000 0.026186 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012300 0.00000