HEADER TRANSFERASE 07-FEB-00 1EF4 TITLE SOLUTION STRUCTURE OF THE ESSENTIAL RNA POLYMERASE SUBUNIT RPB10 FROM TITLE 2 METHANOBACTERIUM THERMOAUTOTROPHICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUBUNIT RPB10; COMPND 5 SYNONYM: SUBUNIT N; COMPND 6 EC: 2.7.7.6; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 145262; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS THREE HELIX BUNDLE, ZINC BINDING, STRUCTURAL GENOMICS, PSI, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 NESG, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.D.MACKERETH,C.H.ARROWSMITH,A.M.EDWARDS,L.P.MCINTOSH,NORTHEAST AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 6 22-MAY-24 1EF4 1 REMARK REVDAT 5 16-FEB-22 1EF4 1 REMARK LINK REVDAT 4 24-FEB-09 1EF4 1 VERSN REVDAT 3 25-JAN-05 1EF4 1 JRNL AUTHOR KEYWDS REMARK REVDAT 2 02-AUG-00 1EF4 1 JRNL REVDAT 1 14-JUN-00 1EF4 0 JRNL AUTH C.D.MACKERETH,C.H.ARROWSMITH,A.M.EDWARDS,L.P.MCINTOSH JRNL TITL ZINC-BUNDLE STRUCTURE OF THE ESSENTIAL RNA POLYMERASE JRNL TITL 2 SUBUNIT RPB10 FROM METHANOBACTERIUM THERMOAUTOTROPHICUM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 6316 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 10841539 JRNL DOI 10.1073/PNAS.97.12.6316 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, ARIA 1999 REMARK 3 AUTHORS : BRUNGER (X-PLOR), NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINED USING ARIA AMBIGUOUS AND REMARK 3 UNAMBIGUOUS RESTRAINTS, AND INCLUDING RESTRAINTS FOR DIHEDRAL REMARK 3 ANGLES AND HYDROGEN BOND DISTANCES. ZINC COORDINATION TO CYS 6,9, REMARK 3 43,44 WITH IDEALIZED TETRAHEDRAL RESTRAINTS WERE ADDED IN THE REMARK 3 FINAL ROUNDS OF REFINEMENT; THE COORDINATING LIGANDS AND THEIR REMARK 3 GEOMETRIC ARRANGEMENT WERE IDENTIFIED BASED ON INITIAL NOE- REMARK 3 DERIVED STRUCTURES CALCULATED WITHOUT INCLUSION OF THE METAL REMARK 3 ION. THREE N- TERMINAL RESIDUES (GLY-SER-HIS) REMAINING FROM REMARK 3 CLEAVAGE OF THE HIS-TAG WERE DISORDERED AND NOT INCLUDED IN THE REMARK 3 FINAL ENSEMBLE. REMARK 4 REMARK 4 1EF4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010516. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.00 REMARK 210 PH : 7.50 REMARK 210 IONIC STRENGTH : 150MM_NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM RPB10 U-15N,13C 20MM REMARK 210 DEUTERATED D-TRIS; 0.15M NACL; REMARK 210 2MM BETA- MERCAPTOETHANOL; 99% REMARK 210 D2O, 1% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D METHYL-METHYL 13C_ SEPARATED REMARK 210 NOESY; 2D NOESY; 3D_13C- REMARK 210 SEPARATED_ NOESY; 3D_15N- REMARK 210 SEPARATED_ NOESY; HNHA; 2D CT- REMARK 210 HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6, FELIX 95.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY WITH SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 O VAL A 33 H LEU A 37 1.54 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 VAL A 4 -76.51 65.18 REMARK 500 1 ARG A 5 -178.73 -53.26 REMARK 500 1 SER A 8 -55.96 -179.40 REMARK 500 1 ASP A 29 107.62 -56.72 REMARK 500 1 ARG A 41 132.68 63.63 REMARK 500 1 HIS A 51 -73.89 -87.66 REMARK 500 1 VAL A 52 56.19 34.93 REMARK 500 1 GLU A 53 90.98 -51.18 REMARK 500 2 VAL A 4 -67.88 66.53 REMARK 500 2 ARG A 5 -168.30 -75.18 REMARK 500 2 CYS A 6 -157.56 -58.33 REMARK 500 2 LEU A 7 30.94 84.74 REMARK 500 2 SER A 8 -76.12 -174.83 REMARK 500 2 LYS A 40 150.88 64.97 REMARK 500 2 ARG A 41 148.53 60.27 REMARK 500 2 LEU A 48 -70.14 -70.63 REMARK 500 2 SER A 50 -78.38 -76.82 REMARK 500 2 VAL A 52 68.05 35.57 REMARK 500 3 VAL A 4 159.85 60.69 REMARK 500 3 ARG A 5 -178.20 74.13 REMARK 500 3 SER A 8 -45.16 177.64 REMARK 500 3 LYS A 40 -80.66 59.57 REMARK 500 3 ARG A 46 -39.37 -38.65 REMARK 500 3 VAL A 52 108.77 -41.48 REMARK 500 3 THR A 54 80.59 53.29 REMARK 500 4 VAL A 4 -77.91 64.45 REMARK 500 4 ARG A 5 179.27 -55.86 REMARK 500 4 CYS A 6 -164.38 -57.84 REMARK 500 4 LEU A 7 28.61 93.42 REMARK 500 4 SER A 8 -72.92 173.69 REMARK 500 4 LYS A 40 -171.82 -54.69 REMARK 500 4 ARG A 41 -49.99 84.29 REMARK 500 4 TYR A 42 -23.92 89.77 REMARK 500 4 ILE A 49 -32.70 -39.66 REMARK 500 4 HIS A 51 -77.54 -87.32 REMARK 500 4 VAL A 52 94.43 34.26 REMARK 500 5 VAL A 4 -76.53 64.98 REMARK 500 5 ARG A 5 -179.64 -55.40 REMARK 500 5 SER A 8 -60.18 -179.06 REMARK 500 5 SER A 14 -72.75 -63.20 REMARK 500 5 ASP A 29 109.83 -55.67 REMARK 500 5 ARG A 41 -42.09 -148.54 REMARK 500 5 TYR A 42 -39.10 89.91 REMARK 500 5 SER A 50 -76.84 -86.88 REMARK 500 5 VAL A 52 27.70 44.99 REMARK 500 5 GLU A 53 75.26 47.23 REMARK 500 6 VAL A 4 161.66 60.93 REMARK 500 6 ARG A 5 -161.12 79.83 REMARK 500 6 SER A 8 -61.54 -172.64 REMARK 500 6 LEU A 39 109.89 -41.26 REMARK 500 REMARK 500 THIS ENTRY HAS 181 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 56 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 111.8 REMARK 620 3 CYS A 43 SG 113.9 104.7 REMARK 620 4 CYS A 44 SG 111.1 112.7 102.1 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 56 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TT11 RELATED DB: TARGETDB DBREF 1EF4 A 1 55 UNP O26147 RPON_METTH 1 55 SEQRES 1 A 55 MET ILE PRO VAL ARG CYS LEU SER CYS GLY LYS PRO VAL SEQRES 2 A 55 SER ALA TYR PHE ASN GLU TYR GLN ARG ARG VAL ALA ASP SEQRES 3 A 55 GLY GLU ASP PRO LYS ASP VAL LEU ASP ASP LEU GLY LEU SEQRES 4 A 55 LYS ARG TYR CYS CYS ARG ARG MET LEU ILE SER HIS VAL SEQRES 5 A 55 GLU THR TRP HET ZN A 56 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 SER A 14 ASP A 26 1 13 HELIX 2 2 PRO A 30 LEU A 37 1 8 HELIX 3 3 CYS A 43 LEU A 48 1 6 LINK SG CYS A 6 ZN ZN A 56 1555 1555 2.22 LINK SG CYS A 9 ZN ZN A 56 1555 1555 2.23 LINK SG CYS A 43 ZN ZN A 56 1555 1555 2.32 LINK SG CYS A 44 ZN ZN A 56 1555 1555 2.30 SITE 1 AC1 4 CYS A 6 CYS A 9 CYS A 43 CYS A 44 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