PDB Short entry for 1DL6 HEADER GENE REGULATION 08-DEC-99 1DL6 TITLE SOLUTION STRUCTURE OF HUMAN TFIIB N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR II B (TFIIB); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS ZINC RIBBON, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR H.-T.CHEN,P.LEGAULT,J.GLUSHKA,J.G.OMICHINSKI,R.A.SCOTT REVDAT 4 16-FEB-22 1DL6 1 REMARK LINK REVDAT 3 24-FEB-09 1DL6 1 VERSN REVDAT 2 01-APR-03 1DL6 1 JRNL REVDAT 1 18-OCT-00 1DL6 0 JRNL AUTH H.T.CHEN,P.LEGAULT,J.GLUSHKA,J.G.OMICHINSKI,R.A.SCOTT JRNL TITL STRUCTURE OF A (CYS3HIS) ZINC RIBBON, A UBIQUITOUS MOTIF IN JRNL TITL 2 ARCHAEAL AND EUCARYAL TRANSCRIPTION. JRNL REF PROTEIN SCI. V. 9 1743 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 11045620 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, CNS 0.4 REMARK 3 AUTHORS : VARIAN ASSOCIATES, INC. (VNMR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 443 RESTRAINTS, 431 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 12 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1DL6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010177. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3MM HTFIIB N-TERMINAL DOMAIN U REMARK 210 -15N; 50MM PHOSPHATE; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY 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 1.7, NMRDRAW 1.7 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 29 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 15 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 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 1 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 2 LYS A 59 C LYS A 59 OXT 0.200 REMARK 500 3 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 4 LYS A 59 C LYS A 59 OXT 0.202 REMARK 500 5 LYS A 59 C LYS A 59 OXT 0.202 REMARK 500 6 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 7 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 8 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 9 LYS A 59 C LYS A 59 OXT 0.200 REMARK 500 10 LYS A 59 C LYS A 59 OXT 0.202 REMARK 500 11 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 12 LYS A 59 C LYS A 59 OXT 0.202 REMARK 500 13 LYS A 59 C LYS A 59 OXT 0.200 REMARK 500 14 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 15 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 16 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 17 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 18 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 19 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 20 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 21 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 22 LYS A 59 C LYS A 59 OXT 0.201 REMARK 500 23 LYS A 59 C LYS A 59 OXT 0.200 REMARK 500 24 LYS A 59 C LYS A 59 OXT 0.200 REMARK 500 25 LYS A 59 C LYS A 59 OXT 0.201 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 ALA A 9 80.76 -63.93 REMARK 500 1 THR A 14 177.91 61.67 REMARK 500 1 HIS A 18 89.15 -153.09 REMARK 500 1 ARG A 28 122.04 172.04 REMARK 500 1 ASP A 31 -173.05 67.48 REMARK 500 1 GLU A 36 -77.77 -115.09 REMARK 500 1 ILE A 46 93.44 -59.64 REMARK 500 1 SER A 50 33.23 -162.54 REMARK 500 1 TRP A 52 -66.26 66.96 REMARK 500 1 ARG A 53 86.67 68.26 REMARK 500 1 PHE A 55 59.71 -90.12 REMARK 500 1 SER A 56 148.54 62.62 REMARK 500 2 SER A 5 96.26 60.74 REMARK 500 2 ARG A 6 133.04 63.53 REMARK 500 2 LEU A 7 47.37 -171.69 REMARK 500 2 ASP A 8 -42.06 -169.97 REMARK 500 2 ALA A 9 -172.12 62.27 REMARK 500 2 VAL A 13 48.14 -92.36 REMARK 500 2 ASP A 20 40.47 -92.26 REMARK 500 2 ALA A 21 63.56 -155.08 REMARK 500 2 GLU A 36 -83.04 -79.54 REMARK 500 2 ARG A 44 96.68 -66.38 REMARK 500 2 ARG A 53 132.05 63.80 REMARK 500 2 PHE A 55 -171.88 60.85 REMARK 500 2 SER A 56 149.38 62.21 REMARK 500 2 ASN A 57 98.43 59.45 REMARK 500 2 ASP A 58 -55.93 -138.45 REMARK 500 3 THR A 4 -66.23 -131.04 REMARK 500 3 SER A 5 -66.68 -162.84 REMARK 500 3 ARG A 6 -62.07 -148.94 REMARK 500 3 ALA A 9 35.45 -97.85 REMARK 500 3 PRO A 11 79.77 -67.47 REMARK 500 3 ARG A 12 59.59 -101.62 REMARK 500 3 VAL A 13 81.32 -63.67 REMARK 500 3 ASP A 20 31.03 -99.56 REMARK 500 3 ALA A 21 80.76 -152.92 REMARK 500 3 ASP A 26 93.29 42.68 REMARK 500 3 ALA A 29 -44.71 -152.40 REMARK 500 3 GLU A 36 -83.30 -87.99 REMARK 500 3 ASP A 43 83.84 -170.70 REMARK 500 3 ILE A 46 59.21 -93.95 REMARK 500 3 VAL A 48 30.80 -97.48 REMARK 500 3 GLU A 51 -46.81 -141.47 REMARK 500 3 SER A 56 169.01 60.52 REMARK 500 4 SER A 3 33.91 -167.23 REMARK 500 4 SER A 5 79.82 60.84 REMARK 500 4 ASP A 8 79.62 60.65 REMARK 500 4 LEU A 10 147.88 61.96 REMARK 500 4 THR A 14 175.31 72.04 REMARK 500 4 LEU A 23 -178.28 -55.05 REMARK 500 REMARK 500 THIS ENTRY HAS 321 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 60 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 HIS A 18 ND1 106.3 REMARK 620 3 CYS A 34 SG 111.1 108.9 REMARK 620 4 CYS A 37 SG 112.3 112.9 105.3 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 60 DBREF 1DL6 A 2 59 UNP Q00403 TF2B_HUMAN 2 59 SEQRES 1 A 58 ALA SER THR SER ARG LEU ASP ALA LEU PRO ARG VAL THR SEQRES 2 A 58 CYS PRO ASN HIS PRO ASP ALA ILE LEU VAL GLU ASP TYR SEQRES 3 A 58 ARG ALA GLY ASP MET ILE CYS PRO GLU CYS GLY LEU VAL SEQRES 4 A 58 VAL GLY ASP ARG VAL ILE ASP VAL GLY SER GLU TRP ARG SEQRES 5 A 58 THR PHE SER ASN ASP LYS HET ZN A 60 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SHEET 1 A 3 VAL A 24 GLU A 25 0 SHEET 2 A 3 MET A 32 ILE A 33 -1 O ILE A 33 N VAL A 24 SHEET 3 A 3 VAL A 40 VAL A 41 -1 N VAL A 41 O MET A 32 LINK SG CYS A 15 ZN ZN A 60 1555 1555 2.30 LINK ND1 HIS A 18 ZN ZN A 60 1555 1555 2.02 LINK SG CYS A 34 ZN ZN A 60 1555 1555 2.29 LINK SG CYS A 37 ZN ZN A 60 1555 1555 2.30 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