Header list of 1rly.pdb file
Complete list - r 2 2 Bytes
HEADER METAL BINDING PROTEIN 26-NOV-03 1RLY
TITLE RDC-DERIVED MODELS OF THE ZINC RIBBON DOMAIN OF HUMAN GENERAL
TITLE 2 TRANSCRIPTION TFIIB (ZINC BOUND STRUCTURES)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR IIB;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: GENERAL TRANSCRIPTION FACTOR TFIIB, S300-II;
COMPND 5 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: GTF2B, TFIIB, TF2B;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11B
KEYWDS ZINC RIBBON, RUBREDOXIN KNUCKLE, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 25
AUTHOR M.GHOSH,M.IKURA
REVDAT 3 02-MAR-22 1RLY 1 REMARK LINK
REVDAT 2 24-FEB-09 1RLY 1 VERSN
REVDAT 1 25-MAY-04 1RLY 0
JRNL AUTH M.GHOSH,L.M.ELSBY,T.K.MAL,J.M.GOODING,S.G.ROBERTS,M.IKURA
JRNL TITL PROBING ZN2+-BINDING EFFECTS ON THE ZINC-RIBBON DOMAIN OF
JRNL TITL 2 HUMAN GENERAL TRANSCRIPTION FACTOR TFIIB.
JRNL REF BIOCHEM.J. V. 378 317 2004
JRNL REFN ISSN 0264-6021
JRNL PMID 14641108
JRNL DOI 10.1042/BJ20031706
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1C, CNS 1.1
REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 476 RESTRAINTS, 443 ARE DISTANCE CONSTRAINTS, 10 ZINC
REMARK 3 COORDINATION RESTRAINTS,23 1H-15N RDC RESTRAINTS
REMARK 4
REMARK 4 1RLY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-03.
REMARK 100 THE DEPOSITION ID IS D_1000020872.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.6MM TFIIB UNIFORM LABELING
REMARK 210 WITH 15N: U-98% 15N, 20MM [2H4]-
REMARK 210 IMIDAZOLE HYDROCHLORIDE, 2.5MM
REMARK 210 ZNCL2, 5% GLYCEROL, 20MM SODIUM
REMARK 210 SULFATE AT PH 6.5, 95% H2O/5%
REMARK 210 D2O; 0.6MM TFIIB UNIFORM
REMARK 210 LABELING WITH 15N: U-98% 15N,
REMARK 210 20MM [2H4]-IMIDAZOLE
REMARK 210 HYDROCHLORIDE, 2.5MM ZNCL2, 5%
REMARK 210 GLYCEROL, 20MM SODIUM SULFATE AT
REMARK 210 PH 6.5, 12MG/ML OF FILAMENTOUS
REMARK 210 PHAGE, PF1, 95% H2O/5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N IPAP
REMARK 210 HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.0, CNS
REMARK 210 1.1
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 25
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-25
REMARK 465 RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 ALA A 60
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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 HE1 HIS A 18 ZN ZN A 61 0.54
REMARK 500 NE2 HIS A 18 HB2 GLU A 36 1.46
REMARK 500 O CYS A 34 H GLY A 38 1.48
REMARK 500 O CYS A 34 N GLY A 38 2.15
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 1 ARG A 6 -74.67 -108.15
REMARK 500 1 ASP A 8 48.32 -153.78
REMARK 500 1 ALA A 9 -55.76 -174.28
REMARK 500 1 ARG A 12 -151.27 -68.16
REMARK 500 1 VAL A 13 -65.15 -133.37
REMARK 500 1 THR A 14 -166.08 169.29
REMARK 500 1 ASP A 26 96.96 55.19
REMARK 500 1 TYR A 27 93.61 -68.11
REMARK 500 1 ALA A 29 35.20 97.71
REMARK 500 1 ASP A 31 -140.57 -98.05
REMARK 500 1 PRO A 35 -17.17 -46.77
REMARK 500 1 ASP A 43 -43.48 177.11
REMARK 500 1 ARG A 44 -111.60 -65.67
REMARK 500 1 VAL A 45 -0.47 72.79
REMARK 500 1 ILE A 46 178.96 47.36
REMARK 500 1 SER A 50 -35.65 173.40
REMARK 500 1 TRP A 52 -86.78 57.18
REMARK 500 1 ARG A 53 82.42 51.42
REMARK 500 1 SER A 56 162.78 60.12
REMARK 500 2 ARG A 6 -65.70 -134.15
REMARK 500 2 LEU A 7 48.40 -164.89
REMARK 500 2 ASP A 8 -72.49 67.81
REMARK 500 2 VAL A 13 81.86 -160.48
REMARK 500 2 PRO A 19 39.78 -73.53
REMARK 500 2 ASP A 20 -52.67 -146.96
REMARK 500 2 LEU A 23 138.66 -34.01
REMARK 500 2 GLU A 25 78.67 -65.81
REMARK 500 2 ASP A 26 -123.95 -157.23
REMARK 500 2 TYR A 27 68.20 71.97
REMARK 500 2 ASP A 31 -92.36 95.30
REMARK 500 2 PRO A 35 -6.83 -52.63
REMARK 500 2 LEU A 39 -147.95 -65.91
REMARK 500 2 VAL A 41 132.59 -173.38
REMARK 500 2 ILE A 46 -72.94 -133.36
REMARK 500 2 ASP A 47 93.98 41.94
REMARK 500 2 SER A 50 -37.57 179.95
REMARK 500 2 TRP A 52 -61.43 69.32
REMARK 500 2 ARG A 53 107.67 77.00
REMARK 500 2 PHE A 55 50.13 -95.90
REMARK 500 2 SER A 56 177.20 62.07
REMARK 500 3 THR A 4 75.14 -150.81
REMARK 500 3 ARG A 6 -70.84 -114.15
REMARK 500 3 LEU A 7 40.96 173.22
REMARK 500 3 ASP A 8 -54.05 77.20
REMARK 500 3 PRO A 11 -80.23 -87.92
REMARK 500 3 THR A 14 -179.61 -175.40
REMARK 500 3 PRO A 19 35.54 -72.82
REMARK 500 3 ASP A 20 -6.02 -153.76
REMARK 500 3 GLU A 25 86.00 -60.69
REMARK 500 3 ASP A 26 120.43 100.17
REMARK 500
REMARK 500 THIS ENTRY HAS 528 RAMACHANDRAN OUTLIERS.
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 61 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 15 SG
REMARK 620 2 HIS A 18 ND1 98.5
REMARK 620 3 HIS A 18 NE2 110.2 68.7
REMARK 620 4 HIS A 18 CE1 116.9 31.8 39.7
REMARK 620 5 CYS A 34 SG 47.1 111.4 73.6 103.8
REMARK 620 6 CYS A 37 SG 90.5 130.9 150.2 146.0 109.8
REMARK 620 N 1 2 3 4 5
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 61
DBREF 1RLY A 1 60 UNP Q00403 TF2B_HUMAN 1 60
SEQRES 1 A 60 MET ALA SER THR SER ARG LEU ASP ALA LEU PRO ARG VAL
SEQRES 2 A 60 THR CYS PRO ASN HIS PRO ASP ALA ILE LEU VAL GLU ASP
SEQRES 3 A 60 TYR ARG ALA GLY ASP MET ILE CYS PRO GLU CYS GLY LEU
SEQRES 4 A 60 VAL VAL GLY ASP ARG VAL ILE ASP VAL GLY SER GLU TRP
SEQRES 5 A 60 ARG THR PHE SER ASN ASP LYS ALA
HET ZN A 61 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
SHEET 1 A 2 MET A 32 ILE A 33 0
SHEET 2 A 2 VAL A 40 VAL A 41 -1 O VAL A 41 N MET A 32
SSBOND 1 CYS A 15 CYS A 34 1555 1555 1.84
LINK SG CYS A 15 ZN ZN A 61 1555 1555 2.30
LINK ND1 HIS A 18 ZN ZN A 61 1555 1555 1.98
LINK NE2 HIS A 18 ZN ZN A 61 1555 1555 1.86
LINK CE1 HIS A 18 ZN ZN A 61 1555 1555 0.88
LINK SG CYS A 34 ZN ZN A 61 1555 1555 2.31
LINK SG CYS A 37 ZN ZN A 61 1555 1555 2.29
SITE 1 AC1 4 CYS A 15 HIS A 18 CYS A 34 CYS A 37
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - r 2 2 Bytes