PDB Short entry for 3FYL HEADER TRANSCRIPTION/DNA 22-JAN-09 3FYL TITLE GR DNA BINDING DOMAIN:CGT COMPLEX 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(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)- COMPND 9 3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: GLUCOCORTICOID RECEPTOR BINDING SITE - CGT TOP STRAND; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)- COMPND 15 3'); COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: GLUCOCORTICOID RECEPTOR BINDING SITE - CGT BOTTOM COMPND 19 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 21-FEB-24 3FYL 1 REMARK SEQADV REVDAT 3 01-NOV-17 3FYL 1 REMARK REVDAT 2 02-JUN-09 3FYL 1 JRNL REVDAT 1 21-APR-09 3FYL 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. 1.63 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 65.9 REMARK 3 NUMBER OF REFLECTIONS : 29316 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.290 REMARK 3 FREE R VALUE TEST SET COUNT : 1844 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 35.2483 - 3.5146 0.99 4299 294 0.1752 0.2221 REMARK 3 2 3.5146 - 2.7900 0.98 4116 272 0.2016 0.2381 REMARK 3 3 2.7900 - 2.4374 0.97 4053 270 0.2085 0.2453 REMARK 3 4 2.4374 - 2.2146 0.94 3908 259 0.1919 0.2134 REMARK 3 5 2.2146 - 2.0559 0.90 3744 254 0.2023 0.2038 REMARK 3 6 2.0559 - 1.9347 0.72 2996 200 0.2206 0.2708 REMARK 3 7 1.9347 - 1.8378 0.49 2010 141 0.2395 0.2812 REMARK 3 8 1.8378 - 1.7578 0.29 1211 80 0.2465 0.2941 REMARK 3 9 1.7578 - 1.6901 0.18 741 50 0.2278 0.3005 REMARK 3 10 1.6901 - 1.6300 0.10 394 24 0.2852 0.4054 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 : 64.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.570 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 1.538 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): 20.0257 -17.0566 -0.1091 REMARK 3 T TENSOR REMARK 3 T11: 0.1105 T22: 0.2513 REMARK 3 T33: 0.2419 T12: 0.0165 REMARK 3 T13: -0.0369 T23: -0.0346 REMARK 3 L TENSOR REMARK 3 L11: 1.3785 L22: 1.4511 REMARK 3 L33: 0.9664 L12: 0.3016 REMARK 3 L13: 0.1081 L23: -0.7197 REMARK 3 S TENSOR REMARK 3 S11: 0.1276 S12: -0.0138 S13: -0.2898 REMARK 3 S21: -0.0758 S22: -0.0529 S23: 0.1628 REMARK 3 S31: 0.0009 S32: -0.1535 S33: -0.0627 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 35.5343 -21.0306 21.5348 REMARK 3 T TENSOR REMARK 3 T11: 0.2598 T22: 0.4384 REMARK 3 T33: 0.2227 T12: 0.0506 REMARK 3 T13: -0.1102 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.0680 L22: 0.2481 REMARK 3 L33: 0.6391 L12: -0.4796 REMARK 3 L13: -0.5971 L23: 0.3352 REMARK 3 S TENSOR REMARK 3 S11: -0.1976 S12: -0.4699 S13: 0.1027 REMARK 3 S21: 0.2018 S22: 0.1553 S23: -0.3512 REMARK 3 S31: 0.1117 S32: 0.2956 S33: 0.0499 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 14.4532 -15.4172 17.8498 REMARK 3 T TENSOR REMARK 3 T11: 0.3507 T22: 0.7033 REMARK 3 T33: 0.2135 T12: 0.1452 REMARK 3 T13: 0.0296 T23: 0.0499 REMARK 3 L TENSOR REMARK 3 L11: 2.9440 L22: 2.5247 REMARK 3 L33: 2.7923 L12: -1.1117 REMARK 3 L13: 2.2493 L23: -1.7731 REMARK 3 S TENSOR REMARK 3 S11: -0.2508 S12: -0.7000 S13: -0.5122 REMARK 3 S21: 0.4986 S22: 0.5873 S23: 0.1556 REMARK 3 S31: -0.8970 S32: -1.0186 S33: -0.2678 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 16.3979 -18.3236 21.5715 REMARK 3 T TENSOR REMARK 3 T11: 0.3150 T22: 0.8609 REMARK 3 T33: 0.3113 T12: 0.0739 REMARK 3 T13: 0.0081 T23: 0.1665 REMARK 3 L TENSOR REMARK 3 L11: 0.6666 L22: 2.1676 REMARK 3 L33: 2.9629 L12: -2.1190 REMARK 3 L13: 2.5945 L23: -1.4000 REMARK 3 S TENSOR REMARK 3 S11: -0.2170 S12: -1.0842 S13: -0.6218 REMARK 3 S21: 0.4059 S22: 0.5987 S23: 0.2723 REMARK 3 S31: -0.4037 S32: -0.9574 S33: -0.3185 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 3FYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051199. 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 : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115889 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 : 31824 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 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 (%) : 71.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.03700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 12.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.53400 REMARK 200 R SYM FOR SHELL (I) : 0.39600 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS, PH 8.5, 100MM KCL, 10MM REMARK 280 MGCL2, 30% 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 58.72250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.72250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.88500 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: 5530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 436 REMARK 465 LYS A 511 REMARK 465 THR A 512 REMARK 465 LYS A 513 REMARK 465 LYS A 514 REMARK 465 LYS A 515 REMARK 465 ILE A 516 REMARK 465 LYS A 517 REMARK 465 GLY A 518 REMARK 465 ILE A 519 REMARK 465 GLN A 520 REMARK 465 GLN A 521 REMARK 465 ALA A 522 REMARK 465 THR A 523 REMARK 465 ALA A 524 REMARK 465 GLY A 525 REMARK 465 GLY B 436 REMARK 465 LYS B 513 REMARK 465 LYS B 514 REMARK 465 LYS B 515 REMARK 465 ILE B 516 REMARK 465 LYS B 517 REMARK 465 GLY B 518 REMARK 465 ILE B 519 REMARK 465 GLN B 520 REMARK 465 GLN B 521 REMARK 465 ALA B 522 REMARK 465 THR B 523 REMARK 465 ALA B 524 REMARK 465 GLY B 525 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 437 OG REMARK 470 LYS B 511 CG CD CE NZ REMARK 470 THR B 512 OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: 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 440 CB CYS A 440 SG -0.104 REMARK 500 DA C 2 C5 DA C 2 C6 0.065 REMARK 500 DA C 2 N7 DA C 2 C8 0.052 REMARK 500 DT C 8 C1' DT C 8 N1 0.080 REMARK 500 DT C 9 N3 DT C 9 C4 -0.059 REMARK 500 DT D 11 O3' DG D 12 P -0.075 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 C 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 1 C2 - N3 - C4 ANGL. DEV. = -5.6 DEGREES REMARK 500 DA C 1 C5 - C6 - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA C 2 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA C 2 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT C 8 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT C 9 C6 - N1 - C2 ANGL. DEV. = -3.4 DEGREES REMARK 500 DT C 9 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DT C 10 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT C 10 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT C 10 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DC D 2 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DG D 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA D 5 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA D 9 O4' - C1' - N9 ANGL. DEV. = -5.8 DEGREES REMARK 500 DA D 9 N1 - C6 - N6 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA D 10 C5 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG D 12 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DG D 12 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT D 13 O3' - P - OP2 ANGL. DEV. = 6.6 DEGREES REMARK 500 DT D 13 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DC D 15 O4' - C1' - C2' ANGL. DEV. = 3.6 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = -7.5 DEGREES REMARK 500 DC D 15 C6 - N1 - C2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC D 15 C4 - C5 - C6 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC D 15 C5 - C6 - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT D 16 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DT D 16 N3 - C4 - O4 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT D 16 C5 - C4 - O4 ANGL. DEV. = -5.8 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 ASN A 473 63.67 -56.61 REMARK 500 ASP A 481 35.71 -144.19 REMARK 500 GLU A 508 33.05 -90.70 REMARK 500 CYS B 450 76.64 -101.19 REMARK 500 ARG B 479 18.42 -146.94 REMARK 500 ASP B 481 44.24 -152.28 REMARK 500 GLU B 508 56.45 -93.46 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 113.8 REMARK 620 3 CYS A 457 SG 113.3 105.8 REMARK 620 4 CYS A 460 SG 108.7 111.0 103.8 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 101.4 REMARK 620 3 CYS A 492 SG 113.7 115.4 REMARK 620 4 CYS A 495 SG 110.3 109.6 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 526 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 440 SG REMARK 620 2 CYS B 443 SG 110.6 REMARK 620 3 CYS B 457 SG 114.6 107.9 REMARK 620 4 CYS B 460 SG 109.3 109.4 104.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 527 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 476 SG REMARK 620 2 CYS B 482 SG 106.7 REMARK 620 3 CYS B 492 SG 111.5 113.9 REMARK 620 4 CYS B 495 SG 107.8 109.4 107.3 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 527 DBREF 3FYL A 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3FYL B 440 525 UNP P06536 GCR_RAT 440 525 DBREF 3FYL C 1 16 PDB 3FYL 3FYL 1 16 DBREF 3FYL D 1 16 PDB 3FYL 3FYL 1 16 SEQADV 3FYL GLY A 436 UNP P06536 EXPRESSION TAG SEQADV 3FYL SER A 437 UNP P06536 EXPRESSION TAG SEQADV 3FYL HIS A 438 UNP P06536 EXPRESSION TAG SEQADV 3FYL MET A 439 UNP P06536 EXPRESSION TAG SEQADV 3FYL GLY B 436 UNP P06536 EXPRESSION TAG SEQADV 3FYL SER B 437 UNP P06536 EXPRESSION TAG SEQADV 3FYL HIS B 438 UNP P06536 EXPRESSION TAG SEQADV 3FYL 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 C 16 DA DA DG DA DA DC DA DT DT DT DT DG DT SEQRES 2 C 16 DC DC DG SEQRES 1 D 16 DT DC DG DG DA DC DA DA DA DA DT DG DT SEQRES 2 D 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 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 ZN 4(ZN 2+) FORMUL 7 EDO C2 H6 O2 FORMUL 10 HOH *160(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 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 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 2.35 LINK SG CYS A 443 ZN ZN A 526 1555 1555 2.35 LINK SG CYS A 457 ZN ZN A 526 1555 1555 2.38 LINK SG CYS A 460 ZN ZN A 526 1555 1555 2.22 LINK SG CYS A 476 ZN ZN A 527 1555 1555 2.29 LINK SG CYS A 482 ZN ZN A 527 1555 1555 2.23 LINK SG CYS A 492 ZN ZN A 527 1555 1555 2.37 LINK SG CYS A 495 ZN ZN A 527 1555 1555 2.31 LINK SG CYS B 440 ZN ZN B 526 1555 1555 2.36 LINK SG CYS B 443 ZN ZN B 526 1555 1555 2.34 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 2.27 LINK SG CYS B 482 ZN ZN B 527 1555 1555 2.20 LINK SG CYS B 492 ZN ZN B 527 1555 1555 2.40 LINK SG CYS B 495 ZN ZN B 527 1555 1555 2.28 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 5 MET A 439 SER A 444 CYS A 476 GLY A 478 SITE 2 AC3 5 ASN A 480 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 CRYST1 117.445 37.770 96.679 90.00 123.50 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 0.008515 0.000000 0.005636 0.00000 SCALE2 0.000000 0.026476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012404 0.00000