HEADER TRANSCRIPTION/DNA 12-FEB-09 3G8U TITLE DNA BINDING DOMAIN:GILZ 16BP COMPLEX-5 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*GP*GP*AP*AP*CP*CP*CP*AP*AP*TP*GP*TP*TP*CP*T)- COMPND 9 3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: GLUCOCORTICOID RECEPTOR BINDING SITE GILZ BOTTOM COMPND 13 STRAND; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*GP*GP*GP*TP*TP*CP*C)- COMPND 16 3'); COMPND 17 CHAIN: C; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: GLUCOCORTICOID RECEPTOR BINDING SITE GILZ 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 3G8U 1 REMARK SEQADV REVDAT 3 01-NOV-17 3G8U 1 REMARK REVDAT 2 02-JUN-09 3G8U 1 JRNL REVDAT 1 21-APR-09 3G8U 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) : 29.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 25403 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.380 REMARK 3 FREE R VALUE TEST SET COUNT : 1874 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 29.2027 - 4.0938 0.99 2798 228 0.1975 0.2268 REMARK 3 2 4.0938 - 3.2508 0.99 2695 221 0.1935 0.2038 REMARK 3 3 3.2508 - 2.8403 0.99 2707 211 0.2260 0.2653 REMARK 3 4 2.8403 - 2.5807 0.98 2637 206 0.2084 0.2382 REMARK 3 5 2.5807 - 2.3959 0.96 2613 210 0.2155 0.2334 REMARK 3 6 2.3959 - 2.2547 0.94 2535 203 0.2049 0.2263 REMARK 3 7 2.2547 - 2.1418 0.90 2430 191 0.2326 0.2741 REMARK 3 8 2.1418 - 2.0486 0.85 2267 174 0.2435 0.2444 REMARK 3 9 2.0486 - 1.9697 0.65 1733 151 0.2673 0.3367 REMARK 3 10 1.9697 - 1.9000 0.41 1114 79 0.2960 0.3183 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 : 82.46 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 82.98 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 : 1.462 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): 19.6338 -13.7244 -0.9354 REMARK 3 T TENSOR REMARK 3 T11: 0.1956 T22: 0.2157 REMARK 3 T33: 0.5278 T12: 0.0513 REMARK 3 T13: 0.0044 T23: -0.1084 REMARK 3 L TENSOR REMARK 3 L11: 5.6675 L22: 1.1550 REMARK 3 L33: 2.3677 L12: -1.5847 REMARK 3 L13: 1.3303 L23: -1.2397 REMARK 3 S TENSOR REMARK 3 S11: 0.3281 S12: 0.1859 S13: -1.3562 REMARK 3 S21: -0.0081 S22: -0.1922 S23: 0.5705 REMARK 3 S31: -0.0414 S32: -0.2550 S33: -0.1032 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 35.3555 -19.1384 20.7698 REMARK 3 T TENSOR REMARK 3 T11: 0.6319 T22: 0.5117 REMARK 3 T33: 0.3661 T12: -0.1689 REMARK 3 T13: -0.0952 T23: 0.1316 REMARK 3 L TENSOR REMARK 3 L11: 2.8597 L22: 2.1498 REMARK 3 L33: 1.0906 L12: -1.4126 REMARK 3 L13: -0.3567 L23: -2.5133 REMARK 3 S TENSOR REMARK 3 S11: -0.2355 S12: -0.8087 S13: -0.1526 REMARK 3 S21: 0.8381 S22: -0.2177 S23: -0.3691 REMARK 3 S31: -0.8896 S32: 0.4795 S33: 0.3354 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 14.3411 -13.1466 18.1510 REMARK 3 T TENSOR REMARK 3 T11: 0.7697 T22: 0.9178 REMARK 3 T33: 0.4780 T12: 0.3793 REMARK 3 T13: -0.0907 T23: -0.1037 REMARK 3 L TENSOR REMARK 3 L11: 3.8981 L22: 1.6773 REMARK 3 L33: 5.2838 L12: -1.9531 REMARK 3 L13: 1.5322 L23: -4.4848 REMARK 3 S TENSOR REMARK 3 S11: -0.6227 S12: -1.0359 S13: -0.7131 REMARK 3 S21: 0.8724 S22: 1.1242 S23: 0.3797 REMARK 3 S31: -1.7037 S32: -1.3475 S33: -0.3896 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 16.1462 -16.0270 21.7271 REMARK 3 T TENSOR REMARK 3 T11: 0.4668 T22: 1.0535 REMARK 3 T33: 0.5080 T12: 0.0994 REMARK 3 T13: -0.0601 T23: 0.2640 REMARK 3 L TENSOR REMARK 3 L11: -0.9527 L22: 3.0650 REMARK 3 L33: 2.1346 L12: -2.2023 REMARK 3 L13: 0.4159 L23: -1.5622 REMARK 3 S TENSOR REMARK 3 S11: -0.4999 S12: -1.0233 S13: -0.5336 REMARK 3 S21: 0.5605 S22: 0.5713 S23: 0.6152 REMARK 3 S31: -0.7423 S32: -0.6084 S33: -0.0718 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 3G8U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : 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) : 1.115878 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 : 27207 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 13.4000 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 (%) : 56.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : 0.62400 REMARK 200 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 (%): 60.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES, PH 5.6, 200MM KCL, 10MM REMARK 280 MGCL2, 5% PEG 8000, 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 58.47050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.30250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.47050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.30250 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: 12390 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 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 HIS B 438 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH D 18 O HOH D 51 2.03 REMARK 500 O HOH A 40 O HOH D 41 2.17 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 CYS A 495 CB CYS A 495 SG 0.108 REMARK 500 DT D 11 C5' DT D 11 C4' 0.046 REMARK 500 DT D 11 C1' DT D 11 N1 0.082 REMARK 500 DG D 12 P DG D 12 O5' 0.070 REMARK 500 DG D 12 C5' DG D 12 C4' 0.082 REMARK 500 DT D 13 O3' DT D 13 C3' -0.039 REMARK 500 DT D 14 O3' DT D 14 C3' -0.036 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 496 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT D 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC D 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT D 11 C5' - C4' - C3' ANGL. DEV. = 7.8 DEGREES REMARK 500 DT D 11 N3 - C4 - O4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG D 12 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DG D 12 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG D 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT D 13 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = -8.6 DEGREES REMARK 500 DT D 14 N3 - C4 - O4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 16 O5' - C5' - C4' ANGL. DEV. = -8.6 DEGREES REMARK 500 DT D 16 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DT D 16 C5' - C4' - C3' ANGL. DEV. = 7.5 DEGREES REMARK 500 DT D 16 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 DT D 16 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 DT D 16 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA C 1 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 DA C 1 O4' - C1' - C2' ANGL. DEV. = 4.3 DEGREES REMARK 500 DA C 1 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA C 1 C2 - N3 - C4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA C 1 C5 - C6 - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA C 2 O5' - P - OP2 ANGL. DEV. = -6.4 DEGREES REMARK 500 DA C 2 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG C 3 C3' - C2' - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 DG C 3 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DA C 5 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DT C 8 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT C 9 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 DG C 11 O4' - C1' - C2' ANGL. DEV. = 3.4 DEGREES REMARK 500 DG C 12 O3' - P - OP1 ANGL. DEV. = 8.5 DEGREES REMARK 500 DG C 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC C 16 C3' - C2' - C1' ANGL. DEV. = -5.2 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 -2.06 -146.19 REMARK 500 ASN A 473 49.26 -96.17 REMARK 500 ASN A 480 34.67 34.54 REMARK 500 ASP A 481 33.76 -143.91 REMARK 500 ASP A 485 -163.94 -113.64 REMARK 500 VAL B 442 -66.99 -96.50 REMARK 500 SER B 444 24.46 45.09 REMARK 500 ASP B 445 -148.60 -64.05 REMARK 500 GLN B 471 -23.07 74.20 REMARK 500 HIS B 472 152.80 -38.94 REMARK 500 ASP B 481 48.98 -151.75 REMARK 500 ASN B 506 136.78 -170.75 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 111.7 REMARK 620 3 CYS A 457 SG 114.6 108.8 REMARK 620 4 CYS A 460 SG 105.8 110.2 105.6 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 101.8 REMARK 620 3 CYS A 492 SG 113.1 116.4 REMARK 620 4 CYS A 495 SG 105.1 111.0 108.7 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 129.4 REMARK 620 3 CYS B 457 SG 114.9 98.8 REMARK 620 4 CYS B 460 SG 108.0 111.8 84.9 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 106.0 REMARK 620 3 CYS B 492 SG 113.8 112.3 REMARK 620 4 CYS B 495 SG 107.2 109.9 107.5 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: 3G6U 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: 3G9M RELATED DB: PDB REMARK 900 RELATED ID: 3G9O RELATED DB: PDB REMARK 900 RELATED ID: 3G9P RELATED DB: PDB DBREF 3G8U A 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G8U B 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3G8U C 1 16 PDB 3G8U 3G8U 1 16 DBREF 3G8U D 1 16 PDB 3G8U 3G8U 1 16 SEQADV 3G8U GLY A 436 UNP P06536 EXPRESSION TAG SEQADV 3G8U SER A 437 UNP P06536 EXPRESSION TAG SEQADV 3G8U HIS A 438 UNP P06536 EXPRESSION TAG SEQADV 3G8U MET A 439 UNP P06536 EXPRESSION TAG SEQADV 3G8U GLY B 436 UNP P06536 EXPRESSION TAG SEQADV 3G8U SER B 437 UNP P06536 EXPRESSION TAG SEQADV 3G8U HIS B 438 UNP P06536 EXPRESSION TAG SEQADV 3G8U 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 DG DG DA DA DC DC DC 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 DG DG DG DT SEQRES 2 C 16 DT DC DC 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 *84(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 ARG B 488 ASN B 491 5 4 HELIX 7 7 CYS B 492 ALA B 503 1 12 SHEET 1 A 2 CYS A 450 HIS A 451 0 SHEET 2 A 2 VAL A 454 LEU A 455 -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 2.41 LINK SG CYS A 443 ZN ZN A 526 1555 1555 2.24 LINK SG CYS A 457 ZN ZN A 526 1555 1555 2.33 LINK SG CYS A 460 ZN ZN A 526 1555 1555 2.33 LINK SG CYS A 476 ZN ZN A 527 1555 1555 2.40 LINK SG CYS A 482 ZN ZN A 527 1555 1555 2.21 LINK SG CYS A 492 ZN ZN A 527 1555 1555 2.29 LINK SG CYS A 495 ZN ZN A 527 1555 1555 2.34 LINK SG CYS B 440 ZN ZN B 526 1555 1555 2.19 LINK SG CYS B 443 ZN ZN B 526 1555 1555 2.39 LINK SG CYS B 457 ZN ZN B 526 1555 1555 2.52 LINK SG CYS B 460 ZN ZN B 526 1555 1555 2.46 LINK SG CYS B 476 ZN ZN B 527 1555 1555 2.23 LINK SG CYS B 482 ZN ZN B 527 1555 1555 2.24 LINK SG CYS B 492 ZN ZN B 527 1555 1555 2.35 LINK SG CYS B 495 ZN ZN B 527 1555 1555 2.39 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 116.941 38.605 98.518 90.00 123.51 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 0.008551 0.000000 0.005662 0.00000 SCALE2 0.000000 0.025903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012174 0.00000