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