HEADER TRANSCRIPTION/DNA 13-FEB-09 3G9M TITLE GR DNA-BINDING DOMAIN:SGK 16BP COMPLEX-44 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*CP*GP*GP*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: GR BINDING SITE: SGK 16 BASE BOTTOM STRAND; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)-3'); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: GR BINDING SITE: SGK 16 BASE 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: NR3C1, GRL; 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 3G9M 1 JRNL REVDAT 1 21-APR-09 3G9M 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. 1.61 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.210 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.5 REMARK 3 NUMBER OF REFLECTIONS : 37875 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.650 REMARK 3 FREE R VALUE TEST SET COUNT : 1760 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 30.6189 - 3.4770 0.89 4110 204 0.1655 0.1529 REMARK 3 2 3.4770 - 2.7603 0.98 4437 217 0.1750 0.2173 REMARK 3 3 2.7603 - 2.4116 0.98 4426 213 0.1673 0.1924 REMARK 3 4 2.4116 - 2.1912 0.89 3977 195 0.2002 0.2490 REMARK 3 5 2.1912 - 2.0341 0.93 4130 201 0.1917 0.2117 REMARK 3 6 2.0341 - 1.9142 0.86 3843 184 0.2416 0.2546 REMARK 3 7 1.9142 - 1.8184 0.74 3288 162 0.2482 0.2642 REMARK 3 8 1.8184 - 1.7392 0.73 3257 155 0.2158 0.1966 REMARK 3 9 1.7392 - 1.6723 0.61 2722 136 0.2318 0.2509 REMARK 3 10 1.6723 - 1.6100 0.43 1925 93 0.2657 0.3015 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 : 71.34 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.560 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.80 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 : 0.010 NULL REMARK 3 ANGLE : 1.328 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): 12.5348 21.3798 40.9794 REMARK 3 T TENSOR REMARK 3 T11: 0.1240 T22: 0.1592 REMARK 3 T33: 0.1837 T12: 0.0028 REMARK 3 T13: 0.0072 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 2.1879 L22: 0.9618 REMARK 3 L33: 0.6025 L12: 0.1441 REMARK 3 L13: 0.5042 L23: 0.2175 REMARK 3 S TENSOR REMARK 3 S11: 0.1148 S12: 0.0774 S13: -0.3338 REMARK 3 S21: -0.0306 S22: -0.0563 S23: -0.1163 REMARK 3 S31: -0.0014 S32: 0.1439 S33: -0.0642 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -3.7920 15.6359 17.8667 REMARK 3 T TENSOR REMARK 3 T11: 0.2720 T22: 0.2713 REMARK 3 T33: 0.1472 T12: -0.0187 REMARK 3 T13: -0.0376 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.8205 L22: 0.4682 REMARK 3 L33: 1.0459 L12: 0.1342 REMARK 3 L13: -0.7218 L23: -0.6851 REMARK 3 S TENSOR REMARK 3 S11: -0.0440 S12: 0.3170 S13: -0.0354 REMARK 3 S21: -0.3110 S22: 0.0699 S23: 0.1350 REMARK 3 S31: 0.0870 S32: -0.3092 S33: -0.0644 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 17.7766 22.2850 22.1713 REMARK 3 T TENSOR REMARK 3 T11: 0.2127 T22: 0.4250 REMARK 3 T33: 0.0738 T12: -0.1282 REMARK 3 T13: 0.0515 T23: -0.0669 REMARK 3 L TENSOR REMARK 3 L11: 2.3504 L22: 1.7064 REMARK 3 L33: 1.9556 L12: 0.7317 REMARK 3 L13: 1.2784 L23: 1.1615 REMARK 3 S TENSOR REMARK 3 S11: -0.1554 S12: 0.7416 S13: -0.3230 REMARK 3 S21: -0.3791 S22: 0.4830 S23: -0.1081 REMARK 3 S31: -0.5692 S32: 0.9721 S33: -0.2583 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 15.8295 19.3511 18.5334 REMARK 3 T TENSOR REMARK 3 T11: 0.1895 T22: 0.6432 REMARK 3 T33: 0.1629 T12: -0.0341 REMARK 3 T13: 0.0372 T23: -0.1522 REMARK 3 L TENSOR REMARK 3 L11: -0.7897 L22: 1.4411 REMARK 3 L33: 3.5982 L12: 1.5317 REMARK 3 L13: 2.1544 L23: 0.7361 REMARK 3 S TENSOR REMARK 3 S11: -0.2436 S12: 0.7597 S13: -0.3056 REMARK 3 S21: -0.2908 S22: 0.4740 S23: -0.2699 REMARK 3 S31: -0.5212 S32: 0.9703 S33: -0.2114 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 3G9M COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-FEB-09. REMARK 100 THE RCSB ID CODE IS RCSB051596. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : 42461 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 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 (%) : 90.4 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56700 REMARK 200 R SYM FOR SHELL (I) : 0.37400 REMARK 200 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: 1GLU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS, PH 7.5, 200MM KCL, 50MM REMARK 280 MGCL2, 10% PEG4000, 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 59.02900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.35650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.02900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.35650 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: 5800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 101 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 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 SER B 437 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 LYS A 514 CG CD CE NZ REMARK 470 LYS B 513 CG CD CE NZ 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 N1 DA C 1 N1 DA C 2 2656 1.84 REMARK 500 OP2 DT D 16 O5' DA C 1 2656 2.06 REMARK 500 C2 DA C 1 N1 DA C 2 2656 2.09 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 DC D 15 O3' DC D 15 C3' -0.087 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 A 510 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT D 1 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG D 3 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG D 3 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DA D 8 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA D 8 N1 - C6 - N6 ANGL. DEV. = 4.7 DEGREES REMARK 500 DA D 9 O4' - C1' - N9 ANGL. DEV. = -6.8 DEGREES REMARK 500 DA D 9 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA D 10 C2 - N3 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT D 11 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 11 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA D 10 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = -9.1 DEGREES REMARK 500 DT D 14 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT D 14 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT D 13 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DC D 15 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = -7.5 DEGREES REMARK 500 DA C 2 N1 - C2 - N3 ANGL. DEV. = -3.5 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT C 8 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT C 9 N3 - C2 - O2 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT C 10 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT C 10 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT C 10 N3 - C2 - O2 ANGL. DEV. = -6.4 DEGREES REMARK 500 DC C 14 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC C 15 O5' - C5' - C4' ANGL. DEV. = -4.9 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 -28.18 -166.40 REMARK 500 HIS A 472 50.44 -140.88 REMARK 500 ASP A 481 38.10 -145.46 REMARK 500 SER B 444 -2.24 72.42 REMARK 500 ASP B 481 45.70 -148.41 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 114.5 107.8 REMARK 620 4 CYS A 460 SG 108.0 111.6 103.9 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 103.8 REMARK 620 3 CYS A 492 SG 113.9 113.9 REMARK 620 4 CYS A 495 SG 109.7 109.7 105.7 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 110.3 REMARK 620 3 CYS B 457 SG 116.0 106.4 REMARK 620 4 CYS B 460 SG 109.7 112.1 102.2 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 104.4 REMARK 620 3 CYS B 492 SG 112.6 113.2 REMARK 620 4 CYS B 495 SG 108.5 110.9 107.2 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 EDO A 528 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 526 REMARK 800 SITE_IDENTIFIER: AC6 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: 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: 3G9I RELATED DB: PDB REMARK 900 RELATED ID: 3G9J RELATED DB: PDB REMARK 900 RELATED ID: 3G9O RELATED DB: PDB REMARK 900 RELATED ID: 3G9P RELATED DB: PDB DBREF 3G9M A 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G9M B 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G9M C 1 16 PDB 3G9M 3G9M 1 16 DBREF 3G9M D 1 16 PDB 3G9M 3G9M 1 16 SEQADV 3G9M GLY A 436 UNP P06536 EXPRESSION TAG SEQADV 3G9M SER A 437 UNP P06536 EXPRESSION TAG SEQADV 3G9M HIS A 438 UNP P06536 EXPRESSION TAG SEQADV 3G9M MET A 439 UNP P06536 EXPRESSION TAG SEQADV 3G9M GLY B 436 UNP P06536 EXPRESSION TAG SEQADV 3G9M SER B 437 UNP P06536 EXPRESSION TAG SEQADV 3G9M HIS B 438 UNP P06536 EXPRESSION TAG SEQADV 3G9M 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 DC DG DG 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 DC DC DG HET ZN A 526 1 HET ZN A 527 1 HET EDO A 1 4 HET EDO A 528 4 HET ZN B 526 1 HET ZN B 527 1 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 ZN 4(ZN 2+) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 11 HOH *254(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 GLN B 471 1 15 HELIX 6 6 ILE B 487 ASN B 491 5 5 HELIX 7 7 CYS B 492 ALA B 503 1 12 HELIX 8 8 GLU B 508 LYS B 515 1 8 SHEET 1 A 2 GLY A 449 HIS A 451 0 SHEET 2 A 2 VAL A 454 THR A 456 -1 O THR A 456 N GLY A 449 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 2.32 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 2.29 LINK SG CYS A 476 ZN ZN A 527 1555 1555 2.36 LINK SG CYS A 482 ZN ZN A 527 1555 1555 2.26 LINK SG CYS A 492 ZN ZN A 527 1555 1555 2.34 LINK SG CYS A 495 ZN ZN A 527 1555 1555 2.35 LINK SG CYS B 440 ZN ZN B 526 1555 1555 2.41 LINK SG CYS B 443 ZN ZN B 526 1555 1555 2.25 LINK SG CYS B 457 ZN ZN B 526 1555 1555 2.42 LINK SG CYS B 460 ZN ZN B 526 1555 1555 2.31 LINK SG CYS B 476 ZN ZN B 527 1555 1555 2.34 LINK SG CYS B 482 ZN ZN B 527 1555 1555 2.27 LINK SG CYS B 492 ZN ZN B 527 1555 1555 2.36 LINK SG CYS B 495 ZN ZN B 527 1555 1555 2.36 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 8 CYS A 476 ALA A 477 GLY A 478 CYS A 482 SITE 2 AC3 8 CYS A 492 HOH A 529 CYS B 482 ASN B 491 SITE 1 AC4 9 HOH A 128 HOH A 220 LYS A 490 ASN A 491 SITE 2 AC4 9 PRO A 493 LYS B 490 ASN B 491 DA D 10 SITE 3 AC4 9 DT D 11 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 CRYST1 118.058 38.713 96.475 90.00 123.71 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 0.008470 0.000000 0.005651 0.00000 SCALE2 0.000000 0.025831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012461 0.00000