HEADER TRANSCRIPTION/DNA 12-DEC-06 2O8K TITLE NMR STRUCTURE OF THE SIGMA-54 RPON DOMAIN BOUND TO THE-24 PROMOTER TITLE 2 ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RNA POLYMERASE SIGMA FACTOR RPON; COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: C-TERMINAL RPON DOMAIN; COMPND 13 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: AQUIFEX AEOLICUS; SOURCE 7 ORGANISM_TAXID: 63363; SOURCE 8 GENE: RPON; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) WITH ROSETTA.PLYSS PLASMID; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PSKB3 KEYWDS PROTEIN-DNA COMPLEX, HELIX-TURN-HELIX, TRANSCRIPTION FACTOR, SIGMA- KEYWDS 2 54, RNA POLYMERASE, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.DOUCLEFF,J.G.PELTON,P.S.LEE,D.E.WEMMER REVDAT 4 27-DEC-23 2O8K 1 REMARK REVDAT 3 16-MAR-22 2O8K 1 REMARK SEQADV REVDAT 2 24-FEB-09 2O8K 1 VERSN REVDAT 1 17-JUL-07 2O8K 0 JRNL AUTH M.DOUCLEFF,J.G.PELTON,P.S.LEE,B.T.NIXON,D.E.WEMMER JRNL TITL STRUCTURAL BASIS OF DNA RECOGNITION BY THE ALTERNATIVE JRNL TITL 2 SIGMA-FACTOR, SIGMA54. JRNL REF J.MOL.BIOL. V. 369 1070 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17481658 JRNL DOI 10.1016/J.JMB.2007.04.019 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.3, X-PLOR 2.14 REMARK 3 AUTHORS : DELAGLIO ET AL. 1995 (NMRPIPE), SCHWIETERS ET AL. REMARK 3 2003 (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PROTEIN AND DNA STRUCTURES DETERMINED REMARK 3 INDIVIDUALLY VIA SIMULATED ANNEALING; THE TWO STRUCTURES WERE REMARK 3 DOCKED USING RIGID BODY MINIMIZATION; THE WHOLE STRUCTURE WAS REMARK 3 REFINED BY SIMULATED ANNEALING REMARK 4 REMARK 4 2O8K COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040822. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 303; 303 REMARK 210 PH : 6.9; 6.9; 6.9 REMARK 210 IONIC STRENGTH : 250 MM NACL; 250 MM NACL; 250 MM REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM SIGMA-54-DNA (U-15N U-13C) REMARK 210 COMPLEX; 250 MM NACL; 10 MM REMARK 210 DEUTERATED-HEPES, PH 6.9; 1 MM REMARK 210 EDTA; 100% D2O; 1 MM SIGMA-54- REMARK 210 DNA (U-15N U-13C) COMPLEX; 250 REMARK 210 MM NACL; 10 MM HEPES, PH 6.9; 1 REMARK 210 MM EDTA; 90% H2O; 10% D2O; 1 MM REMARK 210 SIGMA-54-DNA (U-15N) COMPLEX; REMARK 210 250 MM NACL; 10 MM HEPES, PH 6.9; REMARK 210 1 MM EDTA; 90% H2O; 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_C13-SEPERATED[F1], C12 REMARK 210 -FILTERED[F2] NOESY; 3D_C13- REMARK 210 SEPERATED_NOESY; 3D_15N- REMARK 210 SEPERATED_NOESY; 2D_C12- REMARK 210 FILTERED[F1,F2] NOESY; 2D_C12- REMARK 210 FILTERED[F1] NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.0.4, CYANA 2.1 REMARK 210 METHOD USED : DOCKING, RIGID-BODY REMARK 210 MINIMIZATION, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 STRUCTURES WITH LOWEST ENERGY REMARK 210 AND NO RESTRAINT VIOLATIONS REMARK 210 GREATER THAN 0.5 A AND 5 DEGREES REMARK 210 FOR DISTANCE AND DIHEDRAL REMARK 210 RESTRAINTS, RESPECTIVELY 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 H42 DC B 107 HZ2 LYS A 61 1.29 REMARK 500 H42 DC C 123 HE ARG A 57 1.30 REMARK 500 OD2 ASP A 40 H GLN A 41 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 2 DT B 113 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 9 DT C 121 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 10 DT B 113 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 DT B 113 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 16 DT B 113 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 17 DT B 113 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 19 DT B 103 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 19 DT C 121 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 DT C 121 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES 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 THR A 17 -155.30 -76.35 REMARK 500 1 LYS A 23 23.59 -76.67 REMARK 500 1 GLU A 32 -111.92 -104.07 REMARK 500 1 ASP A 40 -47.14 -22.48 REMARK 500 1 LYS A 53 46.29 19.91 REMARK 500 1 SER A 70 13.09 -171.98 REMARK 500 1 SER A 71 -7.97 61.27 REMARK 500 2 LEU A 16 178.18 -47.47 REMARK 500 2 THR A 17 -159.67 -68.57 REMARK 500 2 GLU A 32 -106.44 -96.12 REMARK 500 2 LYS A 36 77.86 -157.43 REMARK 500 2 ASP A 40 -49.21 -25.72 REMARK 500 2 LYS A 53 40.23 29.30 REMARK 500 2 LEU A 66 -70.56 -64.70 REMARK 500 2 SER A 70 -2.23 -173.03 REMARK 500 2 SER A 71 -29.19 77.80 REMARK 500 2 ARG A 75 -71.28 -89.40 REMARK 500 3 THR A 17 -160.36 -73.07 REMARK 500 3 GLU A 32 -107.26 -94.88 REMARK 500 3 ASP A 40 -47.17 -22.29 REMARK 500 3 LYS A 50 -69.34 -90.13 REMARK 500 3 LYS A 53 37.75 28.12 REMARK 500 3 LEU A 66 -74.17 -72.79 REMARK 500 3 SER A 70 15.88 -170.11 REMARK 500 3 SER A 71 -9.29 60.37 REMARK 500 4 LEU A 16 175.62 -56.01 REMARK 500 4 THR A 17 -159.32 -70.81 REMARK 500 4 GLU A 32 -110.94 -97.46 REMARK 500 4 ASP A 40 -48.74 -20.40 REMARK 500 4 LYS A 50 -63.06 -105.48 REMARK 500 4 LYS A 53 44.77 21.73 REMARK 500 4 LEU A 66 -72.55 -70.44 REMARK 500 4 SER A 71 -14.77 70.25 REMARK 500 5 THR A 17 -159.51 -69.67 REMARK 500 5 LYS A 23 20.98 -76.82 REMARK 500 5 GLU A 32 -109.64 -95.66 REMARK 500 5 ASP A 40 -49.41 -25.37 REMARK 500 5 LYS A 50 -66.21 -102.56 REMARK 500 5 LYS A 53 41.53 23.97 REMARK 500 5 ARG A 63 -7.87 -59.87 REMARK 500 5 LEU A 66 -78.04 -62.95 REMARK 500 5 SER A 70 11.86 -152.74 REMARK 500 5 SER A 71 -7.55 63.12 REMARK 500 6 MET A 15 40.64 38.02 REMARK 500 6 THR A 17 -155.71 -70.08 REMARK 500 6 GLU A 32 -108.00 -92.96 REMARK 500 6 LYS A 36 77.48 -155.78 REMARK 500 6 ASP A 40 -47.61 -25.30 REMARK 500 6 LYS A 50 -68.44 -94.15 REMARK 500 6 LYS A 53 46.83 19.57 REMARK 500 REMARK 500 THIS ENTRY HAS 172 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2O8K A 16 76 UNP O66858 O66858_AQUAE 338 398 DBREF 2O8K B 101 114 PDB 2O8K 2O8K 101 114 DBREF 2O8K C 115 128 PDB 2O8K 2O8K 115 128 SEQADV 2O8K HIS A 14 UNP O66858 CLONING ARTIFACT SEQADV 2O8K MET A 15 UNP O66858 CLONING ARTIFACT SEQRES 1 B 14 DT DT DT DT DG DG DC DA DC DG DT DT DT SEQRES 2 B 14 DC SEQRES 1 C 14 DG DA DA DA DC DG DT DG DC DC DA DA DA SEQRES 2 C 14 DA SEQRES 1 A 63 HIS MET LEU THR GLN GLY GLU LEU MET LYS LEU ILE LYS SEQRES 2 A 63 GLU ILE VAL GLU ASN GLU ASP LYS ARG LYS PRO TYR SER SEQRES 3 A 63 ASP GLN GLU ILE ALA ASN ILE LEU LYS GLU LYS GLY PHE SEQRES 4 A 63 LYS VAL ALA ARG ARG THR VAL ALA LYS TYR ARG GLU MET SEQRES 5 A 63 LEU GLY ILE PRO SER SER ARG GLU ARG ARG ILE HELIX 1 1 LEU A 21 GLU A 30 1 10 HELIX 2 2 SER A 39 GLY A 51 1 13 HELIX 3 3 ALA A 55 GLY A 67 1 13 HELIX 4 4 SER A 71 ILE A 76 1 6 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