HEADER TRANSCRIPTION/DNA 16-JUL-13 2MAP TITLE SOLUTION STRUCTURE OF THE COMPLEX FORMED BY THE REGION 2 OF E. COLI TITLE 2 SIGMAE AND ITS COGNATE -10 PROMOTER ELEMENT NON TEMPLATE STRAND TITLE 3 TGTCAAA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE SIGMA FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: PART OF THE -10 ELEMENT NON TEMPLATE STRAND; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 536056; SOURCE 4 STRAIN: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1; SOURCE 5 GENE: RPOE, ECDH1_1095, ECDH1ME8569_2500; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET26BII; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS ECF SIGMA FACTOR, -10 ELEMENT RECOGNITION, PROTEIN-SSDNA COMPLEX, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR S.CAMPAGNE,J.A.VORHOLT,F.H.-T.ALLAIN REVDAT 5 14-JUN-23 2MAP 1 REMARK SEQADV REVDAT 4 24-JAN-18 2MAP 1 AUTHOR REVDAT 3 19-MAR-14 2MAP 1 JRNL REVDAT 2 26-FEB-14 2MAP 1 JRNL REVDAT 1 19-FEB-14 2MAP 0 JRNL AUTH S.CAMPAGNE,M.E.MARSH,G.CAPITANI,J.A.VORHOLT,F.H.ALLAIN JRNL TITL STRUCTURAL BASIS FOR -10 PROMOTER ELEMENT MELTING BY JRNL TITL 2 ENVIRONMENTALLY INDUCED SIGMA FACTORS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 269 2014 JRNL REFN ISSN 1545-9993 JRNL PMID 24531660 JRNL DOI 10.1038/NSMB.2777 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 3.0, AMBER REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO AND KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000103418. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.07 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN_1, 0.8 MM PROTEIN_2, 90% REMARK 210 H2O/10% D2O; 0.8 MM [U-100% 13C; REMARK 210 U-100% 15N] PROTEIN_1, 0.8 MM REMARK 210 PROTEIN_2, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HN(CO)CA; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D NOESY 1H-1H F1F2F; REMARK 210 2D NOESY 1H-1H F2F REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 1 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT B 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT B 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DT B 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT B 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DA B 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA B 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DT B 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT B 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DA B 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 DG B 2 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DT B 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 DA B 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 5 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 5 DT B 3 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DT B 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DA B 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 6 DG B 2 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 DT B 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DA B 6 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 7 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 7 DA B 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 DA B 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 8 DT B 1 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 8 DT B 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 DG B 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 DT B 3 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 DA B 5 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 8 DA B 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 DA B 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 DT B 1 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 9 DT B 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 108 ANGLE DEVIATIONS. 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 3 SER A 2 -176.32 57.63 REMARK 500 4 LEU A 95 -23.38 -145.00 REMARK 500 7 LEU A 5 26.08 -141.88 REMARK 500 9 GLN A 4 7.33 55.36 REMARK 500 9 LEU A 93 36.56 -144.07 REMARK 500 10 GLN A 4 171.51 57.89 REMARK 500 11 GLN A 4 170.23 59.53 REMARK 500 11 ARG A 92 10.88 55.45 REMARK 500 11 LEU A 93 -0.22 -149.83 REMARK 500 12 LEU A 5 45.05 -88.57 REMARK 500 12 LEU A 93 19.50 54.79 REMARK 500 13 SER A 2 163.02 59.25 REMARK 500 13 GLU A 3 23.23 45.43 REMARK 500 13 ARG A 92 12.12 58.32 REMARK 500 13 LEU A 93 -7.48 -148.88 REMARK 500 14 ARG A 92 19.29 54.56 REMARK 500 14 LEU A 93 32.90 -149.63 REMARK 500 16 LEU A 5 50.85 -97.72 REMARK 500 16 ARG A 91 17.60 -153.84 REMARK 500 16 LEU A 95 -20.23 -145.60 REMARK 500 17 GLN A 4 170.00 58.30 REMARK 500 17 LEU A 5 48.09 -104.90 REMARK 500 17 ARG A 92 139.36 65.20 REMARK 500 18 GLU A 3 -174.98 56.37 REMARK 500 18 LEU A 5 38.66 -79.80 REMARK 500 18 ARG A 92 12.20 57.58 REMARK 500 18 LEU A 95 19.27 55.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MAO RELATED DB: PDB REMARK 900 RELATED ID: 19367 RELATED DB: BMRB DBREF 2MAP A 1 92 UNP C9R146 C9R146_ECOD1 1 92 DBREF 2MAP B 1 7 PDB 2MAP 2MAP 1 7 SEQADV 2MAP LEU A 93 UNP C9R146 EXPRESSION TAG SEQADV 2MAP GLU A 94 UNP C9R146 EXPRESSION TAG SEQADV 2MAP LEU A 95 UNP C9R146 EXPRESSION TAG SEQADV 2MAP VAL A 96 UNP C9R146 EXPRESSION TAG SEQRES 1 A 96 MET SER GLU GLN LEU THR ASP GLN VAL LEU VAL GLU ARG SEQRES 2 A 96 VAL GLN LYS GLY ASP GLN LYS ALA PHE ASN LEU LEU VAL SEQRES 3 A 96 VAL ARG TYR GLN HIS LYS VAL ALA SER LEU VAL SER ARG SEQRES 4 A 96 TYR VAL PRO SER GLY ASP VAL PRO ASP VAL VAL GLN GLU SEQRES 5 A 96 ALA PHE ILE LYS ALA TYR ARG ALA LEU ASP SER PHE ARG SEQRES 6 A 96 GLY ASP SER ALA PHE TYR THR TRP LEU TYR ARG ILE ALA SEQRES 7 A 96 VAL ASN THR ALA LYS ASN TYR LEU VAL ALA GLN GLY ARG SEQRES 8 A 96 ARG LEU GLU LEU VAL SEQRES 1 B 7 DT DG DT DC DA DA DA HELIX 1 1 THR A 6 LYS A 16 1 11 HELIX 2 2 ASP A 18 SER A 38 1 21 HELIX 3 3 ASP A 45 ARG A 59 1 15 HELIX 4 4 ALA A 60 PHE A 64 5 5 HELIX 5 5 ALA A 69 ARG A 91 1 23 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