HEADER TRANSCRIPTION/DNA 06-NOV-15 5EMP
TITLE TRANSCRIPTION FACTOR GRDBD AND MMGRE COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GLUCOCORTICOID RECEPTOR;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 411-500;
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(*CP*CP*AP*GP*AP*AP*CP*AP*TP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3');
COMPND 10 CHAIN: C;
COMPND 11 ENGINEERED: YES;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: DNA (5'-D(P*CP*CP*AP*GP*AP*AP*CP*AP*TP*(5CM)
COMPND 14 P*AP*TP*GP*TP*TP*CP*TP*G)-3');
COMPND 15 CHAIN: D;
COMPND 16 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: NR3C1, GRL;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR
SOURCE 7 PPPHIS4;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1182038;
SOURCE 9 MOL_ID: 2;
SOURCE 10 SYNTHETIC: YES;
SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 12 ORGANISM_TAXID: 32630;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES;
SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 16 ORGANISM_TAXID: 32630
KEYWDS TRANSCRIPTION FACTOR, COMPLEX, DNA, TRANSCRIPTION-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR T.LIAN,J.JIN,X.SU
REVDAT 3 20-MAR-24 5EMP 1 REMARK
REVDAT 2 04-OCT-17 5EMP 1 REMARK
REVDAT 1 29-JUN-16 5EMP 0
JRNL AUTH T.LIAN,J.JIN,X.SU
JRNL TITL THE EFFECTS OF CYTOSINE METHYLATION ON GENERAL TRANSCRIPTION
JRNL TITL 2 FACTORS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.8.1_1168
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.01
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 3 NUMBER OF REFLECTIONS : 20298
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.195
REMARK 3 R VALUE (WORKING SET) : 0.193
REMARK 3 FREE R VALUE : 0.238
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120
REMARK 3 FREE R VALUE TEST SET COUNT : 1039
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 35.0122 - 4.3973 0.99 2908 147 0.1626 0.2227
REMARK 3 2 4.3973 - 3.4913 0.99 2749 165 0.1732 0.2117
REMARK 3 3 3.4913 - 3.0502 0.98 2713 144 0.2068 0.2621
REMARK 3 4 3.0502 - 2.7715 1.00 2754 128 0.2317 0.2648
REMARK 3 5 2.7715 - 2.5729 1.00 2715 161 0.2250 0.2517
REMARK 3 6 2.5729 - 2.4213 1.00 2704 153 0.2367 0.2743
REMARK 3 7 2.4213 - 2.3000 1.00 2716 141 0.2432 0.2720
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 : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.090
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 41.61
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.71
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 : 0.008 1931
REMARK 3 ANGLE : 1.453 2746
REMARK 3 CHIRALITY : 0.073 297
REMARK 3 PLANARITY : 0.004 226
REMARK 3 DIHEDRAL : 25.330 768
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): -11.2051 11.9377 -7.0734
REMARK 3 T TENSOR
REMARK 3 T11: 0.3375 T22: 0.2638
REMARK 3 T33: 0.3050 T12: -0.0353
REMARK 3 T13: 0.0003 T23: 0.0158
REMARK 3 L TENSOR
REMARK 3 L11: 1.1608 L22: 1.3401
REMARK 3 L33: 2.7694 L12: -0.2570
REMARK 3 L13: 0.6405 L23: 0.3888
REMARK 3 S TENSOR
REMARK 3 S11: 0.0813 S12: 0.0257 S13: -0.2647
REMARK 3 S21: -0.1852 S22: 0.0714 S23: 0.0132
REMARK 3 S31: 0.6467 S32: -0.1424 S33: -0.1450
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 5EMP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-15.
REMARK 100 THE DEPOSITION ID IS D_1000215165.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-NOV-13
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 : PHOTON FACTORY
REMARK 200 BEAMLINE : BL-1A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.100
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20343
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 36.584
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 5.200
REMARK 200 R MERGE (I) : 0.08300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7700
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.49800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.170
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
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 (%): 69.85
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS, 200MM KCL, 50MM MGCL2, 10%
REMARK 280 PEG 4000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
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 19.63950
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.02150
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.24600
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.02150
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.63950
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.24600
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: 5910 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12120 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 426
REMARK 465 SER A 427
REMARK 465 HIS A 428
REMARK 465 MET A 429
REMARK 465 THR A 430
REMARK 465 ALA A 431
REMARK 465 THR A 432
REMARK 465 THR A 433
REMARK 465 GLY A 434
REMARK 465 PRO A 435
REMARK 465 PRO A 436
REMARK 465 PRO A 437
REMARK 465 ALA A 509
REMARK 465 ARG A 510
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 GLY B 426
REMARK 465 SER B 427
REMARK 465 HIS B 428
REMARK 465 MET B 429
REMARK 465 THR B 430
REMARK 465 ALA B 431
REMARK 465 THR B 432
REMARK 465 THR B 433
REMARK 465 GLY B 434
REMARK 465 PRO B 435
REMARK 465 PRO B 436
REMARK 465 PRO B 437
REMARK 465 ARG B 510
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 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 GLU A 446 CG CD OE1 OE2
REMARK 470 GLU A 469 CG CD OE1 OE2
REMARK 470 GLN A 471 CG CD OE1 NE2
REMARK 470 ASN A 473 CG OD1 ND2
REMARK 470 GLN B 471 CG CD OE1 NE2
REMARK 470 ASN B 473 CG OD1 ND2
REMARK 470 ALA B 509 CA C O CB
REMARK 470 DT D 10 C7
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 N2 DG C 10 O2 5CM D 11 1.96
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH B 715 O HOH B 725 4555 2.05
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 DA C 8 O3' DT C 9 P -0.090
REMARK 500 DT C 12 O3' DG C 13 P -0.088
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 LYS A 438 N - CA - C ANGL. DEV. = 26.2 DEGREES
REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DA C 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DA C 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DC D 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DT D 16 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 HIS A 472 96.26 37.20
REMARK 500 ASP A 481 42.20 -146.22
REMARK 500 HIS B 472 -64.62 -125.20
REMARK 500 ASP B 481 42.44 -142.51
REMARK 500 GLU B 508 -118.03 63.15
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 601 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 440 SG
REMARK 620 2 CYS A 443 SG 114.5
REMARK 620 3 CYS A 457 SG 110.9 104.5
REMARK 620 4 CYS A 460 SG 110.1 115.6 100.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 602 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 476 SG
REMARK 620 2 CYS A 482 SG 105.4
REMARK 620 3 CYS A 492 SG 110.8 115.7
REMARK 620 4 CYS A 495 SG 110.4 110.1 104.4
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 601 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 440 SG
REMARK 620 2 CYS B 443 SG 110.1
REMARK 620 3 CYS B 457 SG 115.7 106.2
REMARK 620 4 CYS B 460 SG 114.3 110.2 99.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 602 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 476 SG
REMARK 620 2 CYS B 482 SG 103.8
REMARK 620 3 CYS B 492 SG 112.1 114.0
REMARK 620 4 CYS B 495 SG 106.5 110.8 109.3
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 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DT D 10 and 5CM D
REMARK 800 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM D 11 and DA D
REMARK 800 12
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5EMC RELATED DB: PDB
REMARK 900 RELATED ID: 5EMQ RELATED DB: PDB
DBREF 5EMP A 430 519 UNP P04150 GCR_HUMAN 411 500
DBREF 5EMP B 430 519 UNP P04150 GCR_HUMAN 411 500
DBREF 5EMP C 1 18 PDB 5EMP 5EMP 1 18
DBREF 5EMP D 2 19 PDB 5EMP 5EMP 2 19
SEQADV 5EMP GLY A 426 UNP P04150 EXPRESSION TAG
SEQADV 5EMP SER A 427 UNP P04150 EXPRESSION TAG
SEQADV 5EMP HIS A 428 UNP P04150 EXPRESSION TAG
SEQADV 5EMP MET A 429 UNP P04150 EXPRESSION TAG
SEQADV 5EMP GLY B 426 UNP P04150 EXPRESSION TAG
SEQADV 5EMP SER B 427 UNP P04150 EXPRESSION TAG
SEQADV 5EMP HIS B 428 UNP P04150 EXPRESSION TAG
SEQADV 5EMP MET B 429 UNP P04150 EXPRESSION TAG
SEQRES 1 A 94 GLY SER HIS MET THR ALA THR THR GLY PRO PRO PRO LYS
SEQRES 2 A 94 LEU CYS LEU VAL CYS SER ASP GLU ALA SER GLY CYS HIS
SEQRES 3 A 94 TYR GLY VAL LEU THR CYS GLY SER CYS LYS VAL PHE PHE
SEQRES 4 A 94 LYS ARG ALA VAL GLU GLY GLN HIS ASN TYR LEU CYS ALA
SEQRES 5 A 94 GLY ARG ASN ASP CYS ILE ILE ASP LYS ILE ARG ARG LYS
SEQRES 6 A 94 ASN CYS PRO ALA CYS ARG TYR ARG LYS CYS LEU GLN ALA
SEQRES 7 A 94 GLY MET ASN LEU GLU ALA ARG LYS THR LYS LYS LYS ILE
SEQRES 8 A 94 LYS GLY ILE
SEQRES 1 B 94 GLY SER HIS MET THR ALA THR THR GLY PRO PRO PRO LYS
SEQRES 2 B 94 LEU CYS LEU VAL CYS SER ASP GLU ALA SER GLY CYS HIS
SEQRES 3 B 94 TYR GLY VAL LEU THR CYS GLY SER CYS LYS VAL PHE PHE
SEQRES 4 B 94 LYS ARG ALA VAL GLU GLY GLN HIS ASN TYR LEU CYS ALA
SEQRES 5 B 94 GLY ARG ASN ASP CYS ILE ILE ASP LYS ILE ARG ARG LYS
SEQRES 6 B 94 ASN CYS PRO ALA CYS ARG TYR ARG LYS CYS LEU GLN ALA
SEQRES 7 B 94 GLY MET ASN LEU GLU ALA ARG LYS THR LYS LYS LYS ILE
SEQRES 8 B 94 LYS GLY ILE
SEQRES 1 C 18 DC DC DA DG DA DA DC DA DT DG DA DT DG
SEQRES 2 C 18 DT DT DC DT DG
SEQRES 1 D 18 DC DC DA DG DA DA DC DA DT 5CM DA DT DG
SEQRES 2 D 18 DT DT DC DT DG
HET 5CM D 11 20
HET ZN A 601 1
HET ZN A 602 1
HET ZN B 601 1
HET ZN B 602 1
HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
HETNAM ZN ZINC ION
FORMUL 4 5CM C10 H16 N3 O7 P
FORMUL 5 ZN 4(ZN 2+)
FORMUL 9 HOH *47(H2 O)
HELIX 1 AA1 CYS A 457 GLU A 469 1 13
HELIX 2 AA2 ILE A 487 ASN A 491 5 5
HELIX 3 AA3 CYS A 492 GLY A 504 1 13
HELIX 4 AA4 CYS B 457 GLY B 470 1 14
HELIX 5 AA5 CYS B 492 GLY B 504 1 13
SHEET 1 AA1 2 GLY A 449 HIS A 451 0
SHEET 2 AA1 2 VAL A 454 THR A 456 -1 O VAL A 454 N HIS A 451
SHEET 1 AA2 2 GLY B 449 HIS B 451 0
SHEET 2 AA2 2 VAL B 454 THR B 456 -1 O VAL B 454 N HIS B 451
LINK O3' DT D 10 P 5CM D 11 1555 1555 1.59
LINK O3' 5CM D 11 P DA D 12 1555 1555 1.57
LINK SG CYS A 440 ZN ZN A 601 1555 1555 2.27
LINK SG CYS A 443 ZN ZN A 601 1555 1555 2.32
LINK SG CYS A 457 ZN ZN A 601 1555 1555 2.30
LINK SG CYS A 460 ZN ZN A 601 1555 1555 2.31
LINK SG CYS A 476 ZN ZN A 602 1555 1555 2.31
LINK SG CYS A 482 ZN ZN A 602 1555 1555 2.31
LINK SG CYS A 492 ZN ZN A 602 1555 1555 2.32
LINK SG CYS A 495 ZN ZN A 602 1555 1555 2.34
LINK SG CYS B 440 ZN ZN B 601 1555 1555 2.27
LINK SG CYS B 443 ZN ZN B 601 1555 1555 2.38
LINK SG CYS B 457 ZN ZN B 601 1555 1555 2.36
LINK SG CYS B 460 ZN ZN B 601 1555 1555 2.30
LINK SG CYS B 476 ZN ZN B 602 1555 1555 2.32
LINK SG CYS B 482 ZN ZN B 602 1555 1555 2.30
LINK SG CYS B 492 ZN ZN B 602 1555 1555 2.31
LINK SG CYS B 495 ZN ZN B 602 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 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
SITE 1 AC5 5 DT C 9 DG C 10 DA C 11 DA D 9
SITE 2 AC5 5 DA D 12
SITE 1 AC6 5 DT C 9 DG C 10 DA C 11 DT D 10
SITE 2 AC6 5 DT D 13
CRYST1 39.279 100.492 112.043 90.00 90.00 90.00 P 21 21 21 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 0.025459 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009951 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008925 0.00000
(ATOM LINES ARE NOT SHOWN.)
END