PDB Short entry for 1QYP HEADER TRANSCRIPTION 19-AUG-97 1QYP TITLE THERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE II; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUBUNIT RPB9, C-TERMINAL DOMAIN, RESIDUES 58 -110; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS CELER; SOURCE 3 ORGANISM_TAXID: 2264; SOURCE 4 CELL_LINE: BL21; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) LYSS; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15-B KEYWDS TRANSCRIPTION, RNA POLYMERASE II SUBUNIT, RPB9, ZN RIBBON, KEYWDS 2 HYPERTHERMOPHILIC, EXTREMOPHILE EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR B.WANG,D.N.M.JONES,B.P.KAINE,M.A.WEISS REVDAT 4 01-MAY-24 1QYP 1 REMARK LINK REVDAT 3 29-NOV-17 1QYP 1 REMARK HELIX REVDAT 2 24-FEB-09 1QYP 1 VERSN REVDAT 1 24-DEC-97 1QYP 0 JRNL AUTH B.WANG,D.N.JONES,B.P.KAINE,M.A.WEISS JRNL TITL HIGH-RESOLUTION STRUCTURE OF AN ARCHAEAL ZINC RIBBON DEFINES JRNL TITL 2 A GENERAL ARCHITECTURAL MOTIF IN EUKARYOTIC RNA POLYMERASES. JRNL REF STRUCTURE V. 6 555 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9634694 JRNL DOI 10.1016/S0969-2126(98)00058-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.QIAN,C.JEON,H.YOON,K.AGARWAL,M.A.WEISS REMARK 1 TITL ERRATUM. STRUCTURE OF A NEW NUCLEIC-ACID-BINDING MOTIF IN REMARK 1 TITL 2 EUKARYOTIC TRANSCRIPTIONAL ELONGATION FACTOR TFIIS REMARK 1 REF NATURE V. 376 279 1995 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 2 REMARK 1 AUTH X.QIAN,C.JEON,H.YOON,K.AGARWAL,M.A.WEISS REMARK 1 TITL STRUCTURE OF A NEW NUCLEIC-ACID-BINDING MOTIF IN EUKARYOTIC REMARK 1 TITL 2 TRANSCRIPTIONAL ELONGATION FACTOR TFIIS REMARK 1 REF NATURE V. 365 277 1993 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QYP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175946. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 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 HG CYS A 46 ZN ZN A 58 1.48 REMARK 500 H TYR A 27 O LYS A 45 1.50 REMARK 500 HG CYS A 49 ZN ZN A 58 1.57 REMARK 500 H MET A 31 O THR A 41 1.58 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 SER A 2 -39.23 -137.29 REMARK 500 1 GLU A 5 64.41 -163.85 REMARK 500 1 LEU A 8 -53.61 -134.72 REMARK 500 1 LEU A 11 115.91 63.39 REMARK 500 1 LYS A 20 -69.72 -100.69 REMARK 500 1 ASN A 23 172.78 -52.38 REMARK 500 1 THR A 33 -140.08 -126.78 REMARK 500 1 ARG A 34 -91.02 -87.52 REMARK 500 1 ALA A 35 98.12 -179.76 REMARK 500 1 ASP A 37 -59.52 -179.41 REMARK 500 1 GLU A 38 104.25 -164.33 REMARK 500 1 SER A 40 101.19 57.26 REMARK 500 1 CYS A 46 150.08 -49.15 REMARK 500 1 THR A 47 47.33 -100.00 REMARK 500 1 LYS A 48 -69.72 -145.06 REMARK 500 1 TRP A 53 -149.99 -125.62 REMARK 500 1 SER A 55 -138.63 -102.86 REMARK 500 1 TYR A 56 25.72 -153.81 REMARK 500 2 SER A 2 115.65 59.27 REMARK 500 2 HIS A 3 -154.64 -114.52 REMARK 500 2 GLN A 6 -170.59 47.68 REMARK 500 2 LEU A 11 139.82 -176.18 REMARK 500 2 LYS A 20 -73.17 -105.75 REMARK 500 2 GLN A 32 82.51 -157.96 REMARK 500 2 THR A 33 -139.08 -111.71 REMARK 500 2 ARG A 34 -88.17 -109.93 REMARK 500 2 ALA A 35 93.36 46.43 REMARK 500 2 SER A 40 113.19 62.41 REMARK 500 2 THR A 47 49.85 -98.27 REMARK 500 2 LYS A 48 -73.94 -149.66 REMARK 500 2 TRP A 53 -152.35 -125.08 REMARK 500 3 SER A 2 177.29 53.93 REMARK 500 3 MET A 4 123.83 62.21 REMARK 500 3 LYS A 9 -140.95 37.35 REMARK 500 3 ASN A 23 169.81 -47.61 REMARK 500 3 ARG A 34 -78.54 -152.28 REMARK 500 3 ALA A 35 -74.41 -120.87 REMARK 500 3 SER A 40 -79.50 -144.36 REMARK 500 3 THR A 47 53.40 -99.94 REMARK 500 3 LYS A 48 -58.73 -157.20 REMARK 500 3 TRP A 53 -154.44 -124.01 REMARK 500 4 SER A 2 -161.17 -117.07 REMARK 500 4 MET A 4 73.30 49.87 REMARK 500 4 LEU A 8 179.88 56.49 REMARK 500 4 THR A 10 132.80 59.56 REMARK 500 4 LEU A 11 146.18 -175.52 REMARK 500 4 PRO A 12 -163.10 -63.03 REMARK 500 4 ASN A 23 174.68 -55.79 REMARK 500 4 ARG A 34 -94.96 -126.19 REMARK 500 4 ALA A 35 -176.16 47.51 REMARK 500 REMARK 500 THIS ENTRY HAS 335 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 34 0.20 SIDE CHAIN REMARK 500 1 ARG A 54 0.21 SIDE CHAIN REMARK 500 2 ARG A 34 0.32 SIDE CHAIN REMARK 500 2 ARG A 54 0.19 SIDE CHAIN REMARK 500 3 ARG A 34 0.19 SIDE CHAIN REMARK 500 3 ARG A 54 0.28 SIDE CHAIN REMARK 500 4 ARG A 34 0.31 SIDE CHAIN REMARK 500 4 ARG A 54 0.29 SIDE CHAIN REMARK 500 5 ARG A 54 0.14 SIDE CHAIN REMARK 500 6 ARG A 34 0.29 SIDE CHAIN REMARK 500 6 ARG A 54 0.28 SIDE CHAIN REMARK 500 7 ARG A 34 0.22 SIDE CHAIN REMARK 500 7 ARG A 54 0.18 SIDE CHAIN REMARK 500 8 ARG A 34 0.26 SIDE CHAIN REMARK 500 8 ARG A 54 0.32 SIDE CHAIN REMARK 500 9 ARG A 34 0.20 SIDE CHAIN REMARK 500 9 ARG A 54 0.12 SIDE CHAIN REMARK 500 10 ARG A 34 0.29 SIDE CHAIN REMARK 500 10 ARG A 54 0.21 SIDE CHAIN REMARK 500 11 ARG A 34 0.23 SIDE CHAIN REMARK 500 11 ARG A 54 0.29 SIDE CHAIN REMARK 500 12 ARG A 34 0.27 SIDE CHAIN REMARK 500 12 ARG A 54 0.30 SIDE CHAIN REMARK 500 13 ARG A 34 0.22 SIDE CHAIN REMARK 500 13 ARG A 54 0.14 SIDE CHAIN REMARK 500 14 ARG A 34 0.32 SIDE CHAIN REMARK 500 14 ARG A 54 0.30 SIDE CHAIN REMARK 500 15 ARG A 34 0.27 SIDE CHAIN REMARK 500 15 ARG A 54 0.30 SIDE CHAIN REMARK 500 16 ARG A 34 0.29 SIDE CHAIN REMARK 500 16 ARG A 54 0.31 SIDE CHAIN REMARK 500 17 ARG A 34 0.31 SIDE CHAIN REMARK 500 17 ARG A 54 0.31 SIDE CHAIN REMARK 500 18 ARG A 34 0.24 SIDE CHAIN REMARK 500 18 ARG A 54 0.30 SIDE CHAIN REMARK 500 19 ARG A 34 0.19 SIDE CHAIN REMARK 500 19 ARG A 54 0.32 SIDE CHAIN REMARK 500 20 ARG A 34 0.20 SIDE CHAIN REMARK 500 20 ARG A 54 0.22 SIDE CHAIN REMARK 500 21 ARG A 34 0.21 SIDE CHAIN REMARK 500 21 ARG A 54 0.20 SIDE CHAIN REMARK 500 22 ARG A 34 0.31 SIDE CHAIN REMARK 500 22 ARG A 54 0.28 SIDE CHAIN REMARK 500 23 ARG A 34 0.28 SIDE CHAIN REMARK 500 23 ARG A 54 0.22 SIDE CHAIN REMARK 500 24 ARG A 34 0.23 SIDE CHAIN REMARK 500 24 ARG A 54 0.29 SIDE CHAIN REMARK 500 25 ARG A 34 0.20 SIDE CHAIN REMARK 500 25 ARG A 54 0.25 SIDE CHAIN 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 58 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 CYS A 21 SG 109.1 REMARK 620 3 CYS A 46 SG 104.5 112.5 REMARK 620 4 CYS A 49 SG 111.3 108.8 110.6 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 58 DBREF 1QYP A 5 57 UNP Q56254 RPOM_THECE 58 110 SEQRES 1 A 57 GLY SER HIS MET GLU GLN ASP LEU LYS THR LEU PRO THR SEQRES 2 A 57 THR LYS ILE THR CYS PRO LYS CYS GLY ASN ASP THR ALA SEQRES 3 A 57 TYR TRP TRP GLU MET GLN THR ARG ALA GLY ASP GLU PRO SEQRES 4 A 57 SER THR ILE PHE TYR LYS CYS THR LYS CYS GLY HIS THR SEQRES 5 A 57 TRP ARG SER TYR GLU HET ZN A 58 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SHEET 1 B1 4 THR A 13 LYS A 15 0 SHEET 2 B1 4 THR A 25 GLU A 30 -1 SHEET 3 B1 4 THR A 41 CYS A 46 -1 SHEET 4 B1 4 HIS A 51 ARG A 54 -1 LINK SG CYS A 18 ZN ZN A 58 1555 1555 2.30 LINK SG CYS A 21 ZN ZN A 58 1555 1555 2.30 LINK SG CYS A 46 ZN ZN A 58 1555 1555 2.30 LINK SG CYS A 49 ZN ZN A 58 1555 1555 2.30 SITE 1 AC1 5 CYS A 18 CYS A 21 ASN A 23 CYS A 46 SITE 2 AC1 5 CYS A 49 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