PDB Short entry for 1XS9 HEADER TRANSCRIPTION/DNA 18-OCT-04 1XS9 TITLE A MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD OF TITLE 2 RNA POLYMERASE AND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*C COMPND 3 P*AP*T)-3'; COMPND 4 CHAIN: B; COMPND 5 FRAGMENT: PROMOTER REGION; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(P*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*A COMPND 9 P*TP*C)-3'; COMPND 10 CHAIN: C; COMPND 11 FRAGMENT: PROMOTER REGION; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN MARA; COMPND 15 CHAIN: A; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN; COMPND 19 CHAIN: D; COMPND 20 SYNONYM: RNAP ALPHA SUBUNIT, TRANSCRIPTASE ALPHA CHAIN, RNA COMPND 21 POLYMERASE ALPHA SUBUNIT; COMPND 22 EC: 2.7.7.6; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 GENE: MARA; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 14 MOL_ID: 4; SOURCE 15 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 16 ORGANISM_TAXID: 562; SOURCE 17 GENE: RPOA, PEZ, PHS, SEZ; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS PROTEIN-DNA COMPLEX, TERNARY COMPLEX, MARA, RNA POLYMERASE, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR B.DANGI,A.M.GRONENBORN,J.L.ROSNER,R.G.MARTIN REVDAT 3 02-MAR-22 1XS9 1 REMARK SEQADV REVDAT 2 24-FEB-09 1XS9 1 VERSN REVDAT 1 26-OCT-04 1XS9 0 SPRSDE 26-OCT-04 1XS9 1TI9 JRNL AUTH B.DANGI,A.M.GRONENBORN,J.L.ROSNER,R.G.MARTIN JRNL TITL VERSATILITY OF THE CARBOXY-TERMINAL DOMAIN OF THE ALPHA JRNL TITL 2 SUBUNIT OF RNA POLYMERASE IN TRANSCRIPTIONAL ACTIVATION: USE JRNL TITL 3 OF THE DNA CONTACT SITE AS A PROTEIN CONTACT SITE FOR MARA. JRNL REF MOL.MICROBIOL. V. 54 45 2004 JRNL REFN ISSN 0950-382X JRNL PMID 15458404 JRNL DOI 10.1111/J.1365-2958.2004.04250.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : JONES,ZOU,COWAN,KJELDGAARD REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PROGRAM HADDOCK WAS USED TO GENERATE REMARK 3 THE NODELS REMARK 4 REMARK 4 1XS9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030708. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : AS DESCRIBED IN PAPER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XWINNMR, HADDOCK REMARK 210 METHOD USED : MODEL BASED ON CHEMICAL SHIFT REMARK 210 PERTURBATION MAPPING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A, D 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 RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLY D 246 REMARK 465 SER D 247 REMARK 465 HIS D 248 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 O2 DC B 421 H21 DG C 430 1.57 REMARK 500 OE2 GLU A 35 HZ1 LYS A 41 1.59 REMARK 500 H21 DG B 420 O2 DC C 431 1.59 REMARK 500 OD2 ASP A 22 HZ1 LYS D 298 1.60 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 THR A 2 64.33 61.65 REMARK 500 MET A 3 -60.21 -133.62 REMARK 500 ARG A 5 -64.80 -132.59 REMARK 500 HIS A 14 31.61 -79.60 REMARK 500 SER A 15 21.31 -147.80 REMARK 500 SER A 26 -57.02 -133.15 REMARK 500 TYR A 101 -58.79 -123.73 REMARK 500 ASP A 103 -0.57 71.87 REMARK 500 PRO A 123 35.93 -72.21 REMARK 500 HIS A 126 -32.25 -151.62 REMARK 500 ASN A 128 -26.41 73.13 REMARK 500 GLU D 261 73.59 62.36 REMARK 500 LEU D 262 -138.34 -120.33 REMARK 500 SER D 266 -71.54 -168.82 REMARK 500 PRO D 293 66.21 -64.75 REMARK 500 ASN D 294 -47.41 176.33 REMARK 500 TRP D 321 -36.09 -134.67 REMARK 500 PRO D 323 -155.06 -81.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 1XS9 A 1 129 UNP P0ACH5 MARA_ECOLI 1 129 DBREF 1XS9 D 249 329 UNP P0A7Z4 RPOA_ECOLI 249 329 DBREF 1XS9 B 404 423 PDB 1XS9 1XS9 404 423 DBREF 1XS9 C 428 447 PDB 1XS9 1XS9 428 447 SEQADV 1XS9 GLY A -2 UNP P0ACH5 CLONING ARTIFACT SEQADV 1XS9 SER A -1 UNP P0ACH5 CLONING ARTIFACT SEQADV 1XS9 HIS A 0 UNP P0ACH5 CLONING ARTIFACT SEQADV 1XS9 GLY D 246 UNP P0A7Z4 CLONING ARTIFACT SEQADV 1XS9 SER D 247 UNP P0A7Z4 CLONING ARTIFACT SEQADV 1XS9 HIS D 248 UNP P0A7Z4 CLONING ARTIFACT SEQRES 1 B 20 DG DA DT DT DT DA DG DC DA DA DA DA DC SEQRES 2 B 20 DG DT DG DG DC DA DT SEQRES 1 C 20 DA DT DG DC DC DA DC DG DT DT DT DT DG SEQRES 2 C 20 DC DT DA DA DA DT DC SEQRES 1 A 132 GLY SER HIS MET THR MET SER ARG ARG ASN THR ASP ALA SEQRES 2 A 132 ILE THR ILE HIS SER ILE LEU ASP TRP ILE GLU ASP ASN SEQRES 3 A 132 LEU GLU SER PRO LEU SER LEU GLU LYS VAL SER GLU ARG SEQRES 4 A 132 SER GLY TYR SER LYS TRP HIS LEU GLN ARG MET PHE LYS SEQRES 5 A 132 LYS GLU THR GLY HIS SER LEU GLY GLN TYR ILE ARG SER SEQRES 6 A 132 ARG LYS MET THR GLU ILE ALA GLN LYS LEU LYS GLU SER SEQRES 7 A 132 ASN GLU PRO ILE LEU TYR LEU ALA GLU ARG TYR GLY PHE SEQRES 8 A 132 GLU SER GLN GLN THR LEU THR ARG THR PHE LYS ASN TYR SEQRES 9 A 132 PHE ASP VAL PRO PRO HIS LYS TYR ARG MET THR ASN MET SEQRES 10 A 132 GLN GLY GLU SER ARG PHE LEU HIS PRO LEU ASN HIS TYR SEQRES 11 A 132 ASN SER SEQRES 1 D 84 GLY SER HIS PHE ASP PRO ILE LEU LEU ARG PRO VAL ASP SEQRES 2 D 84 ASP LEU GLU LEU THR VAL ARG SER ALA ASN CYS LEU LYS SEQRES 3 D 84 ALA GLU ALA ILE HIS TYR ILE GLY ASP LEU VAL GLN ARG SEQRES 4 D 84 THR GLU VAL GLU LEU LEU LYS THR PRO ASN LEU GLY LYS SEQRES 5 D 84 LYS SER LEU THR GLU ILE LYS ASP VAL LEU ALA SER ARG SEQRES 6 D 84 GLY LEU SER LEU GLY MET ARG LEU GLU ASN TRP PRO PRO SEQRES 7 D 84 ALA SER ILE ALA ASP GLU HELIX 1 1 ASN A 7 THR A 12 1 6 HELIX 2 2 ILE A 16 ASP A 22 1 7 HELIX 3 3 VAL A 33 GLY A 38 5 6 HELIX 4 4 SER A 40 LYS A 50 1 11 HELIX 5 5 SER A 55 GLU A 74 1 20 HELIX 6 6 PRO A 78 GLY A 87 1 10 HELIX 7 7 SER A 90 ASN A 100 1 11 HELIX 8 8 PRO A 105 THR A 112 1 8 HELIX 9 9 PRO D 256 LEU D 260 5 5 HELIX 10 10 SER D 266 LYS D 271 1 6 HELIX 11 11 TYR D 277 VAL D 282 1 6 HELIX 12 12 THR D 285 LEU D 290 1 6 HELIX 13 13 GLY D 296 LYS D 298 5 3 HELIX 14 14 SER D 299 ARG D 310 1 12 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