HEADER TRANSCRIPTION 15-AUG-17 5OR5 TITLE NMR STRUCTURE OF THE COMPLEX FORMED BY AN ENGINEERED REGION 2 OF TITLE 2 SIGMAE IN COMPLEX WITH GTAAAA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECF RNA POLYMERASE SIGMA-E FACTOR,ECF RNA POLYMERASE SIGMA COMPND 3 FACTOR SIGW,ECF RNA POLYMERASE SIGMA-E FACTOR; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: RNA POLYMERASE SIGMA-E FACTOR,SIGMA-24,ECF SIGMA FACTOR COMPND 6 SIGW,ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGW,RNA POLYMERASE COMPND 7 SIGMA-W FACTOR,SIGMA-W FACTOR,RNA POLYMERASE SIGMA-E FACTOR,SIGMA-24; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*TP*AP*AP*AP*A)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12), BACILLUS SOURCE 3 SUBTILIS; SOURCE 4 ORGANISM_TAXID: 83333, 224308; SOURCE 5 STRAIN: K12, 168; SOURCE 6 GENE: RPOE, SIGE, B2573, JW2557, SIGW, YBBL, BSU01730; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS PROMOTER MELTING, -10 ELEMENT RECOGNITION, ECF SIGMA FACTOR, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 13 AUTHOR S.CAMPAGNE,J.A.VORHOLT,F.H.ALLAIN REVDAT 4 15-MAY-24 5OR5 1 REMARK REVDAT 3 10-JUL-19 5OR5 1 JRNL REVDAT 2 08-MAY-19 5OR5 1 REMARK REVDAT 1 27-JUN-18 5OR5 0 JRNL AUTH S.CAMPAGNE,J.A.VORHOLT,F.H.ALLAIN JRNL TITL ENGINEERED PROMOTER SELECTIVITY OF AN ECF SIGMA FACTOR JRNL REF NOT PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.CAMPAGNE,M.E.MARSH,G.CAPITANI,J.A.VORHOLT,F.H.ALLAIN REMARK 1 TITL STRUCTURAL BASIS FOR -10 PROMOTER ELEMENT MELTING BY REMARK 1 TITL 2 ENVIRONMENTALLY INDUCED SIGMA FACTORS. REMARK 1 REF NAT. STRUCT. MOL. BIOL. V. 21 269 2014 REMARK 1 REFN ESSN 1545-9985 REMARK 1 PMID 24531660 REMARK 1 DOI 10.1038/NSMB.2777 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5OR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006230. 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 : 60 REMARK 210 PRESSURE : ATMOSPHERIC ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 ENGINEERED REGION2 OF SIGMAE REMARK 210 FROM E. COLI IN WHICH THE LOOP REMARK 210 L3 WAS REPLACED BY THE LOOP L3 REMARK 210 OF BACILLUS SUBTILIS SIGMAW, 1 REMARK 210 MM DNA (5'-D(*GP*TP*AP*AP*AP*A)- REMARK 210 3'), 10 MM SODIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1 MM [U-99% 13C; U-99% 15N] REMARK 210 ENGINEERED REGION2 OF SIGMAE REMARK 210 FROM E. COLI IN WHICH THE LOOP REMARK 210 L3 WAS REPLACED BY THE LOOP L3 REMARK 210 OF BACILLUS SUBTILIS SIGMAW, 1 REMARK 210 MM DNA (5'-D(*GP*TP*AP*AP*AP*A)- REMARK 210 3'), 10 MM SODIUM PHOSPHATE, 50 REMARK 210 MM SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D REMARK 210 H(CCO)NH; 3D C(CO)NH; 2D 1H-1H REMARK 210 NOESY F2F; 2D 1H-1H NOESY F1FF2F REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CARA, CANDID, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 97 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 98 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 99 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 100 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA B 100 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DA B 99 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DT B 97 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DA B 100 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 5 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DT B 97 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DA B 98 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DA B 101 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 6 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DA B 101 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 7 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 7 DA B 99 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 7 DA B 100 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 DA B 101 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 8 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 8 DA B 101 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 9 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 9 DA B 99 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 9 DA B 100 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 10 DA B 99 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 10 DA B 100 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 10 DA B 101 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 DT B 97 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 11 DA B 99 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 11 DA B 100 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 11 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 12 DT B 97 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 12 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 12 DA B 100 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 12 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 13 DA B 98 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 13 DA B 100 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 13 DA B 101 O4' - C1' - N9 ANGL. DEV. = 2.1 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 SER A 2 172.15 58.66 REMARK 500 1 GLN A 4 -15.79 61.76 REMARK 500 2 GLN A 4 -10.91 -140.47 REMARK 500 5 LEU A 93 -17.50 -141.68 REMARK 500 7 SER A 2 -180.00 57.73 REMARK 500 7 GLN A 4 -14.76 61.69 REMARK 500 8 GLN A 4 -11.32 -140.74 REMARK 500 10 LEU A 93 -4.93 -143.69 REMARK 500 12 GLN A 4 -17.03 60.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LUP RELATED DB: PDB REMARK 900 RELATED ID: 2MAO RELATED DB: PDB REMARK 900 RELATED ID: 2MAP RELATED DB: PDB REMARK 900 RELATED ID: 34172 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE COMPLEX FORMED BY AN ENGINEERED REGION 2 OF REMARK 900 SIGMAE IN COMPLEX WITH GTAAAA DBREF 5OR5 A 1 64 UNP P0AGB6 RPOE_ECOLI 1 64 DBREF 5OR5 A 65 70 UNP Q45585 SIGW_BACSU 64 69 DBREF 5OR5 A 72 92 UNP P0AGB6 RPOE_ECOLI 72 92 DBREF 5OR5 B 96 101 PDB 5OR5 5OR5 96 101 SEQADV 5OR5 SER A 71 UNP Q45585 LINKER SEQADV 5OR5 LEU A 93 UNP P0AGB6 EXPRESSION TAG SEQADV 5OR5 GLU A 94 UNP P0AGB6 EXPRESSION TAG SEQADV 5OR5 LEU A 95 UNP P0AGB6 EXPRESSION TAG SEQRES 1 A 95 MET SER GLU GLN LEU THR ASP GLN VAL LEU VAL GLU ARG SEQRES 2 A 95 VAL GLN LYS GLY ASP GLN LYS ALA PHE ASN LEU LEU VAL SEQRES 3 A 95 VAL ARG TYR GLN HIS LYS VAL ALA SER LEU VAL SER ARG SEQRES 4 A 95 TYR VAL PRO SER GLY ASP VAL PRO ASP VAL VAL GLN GLU SEQRES 5 A 95 ALA PHE ILE LYS ALA TYR ARG ALA LEU ASP SER PHE ASP SEQRES 6 A 95 ILE ASN ARG LYS PHE SER THR TRP LEU TYR ARG ILE ALA SEQRES 7 A 95 VAL ASN THR ALA LYS ASN TYR LEU VAL ALA GLN GLY ARG SEQRES 8 A 95 ARG LEU GLU LEU SEQRES 1 B 6 GNG DT DA DA DA DA HET GNG B 96 31 HETNAM GNG 2'-DEOXY-GUANOSINE FORMUL 2 GNG C10 H13 N5 O4 HELIX 1 AA1 THR A 6 GLY A 17 1 12 HELIX 2 AA2 ASP A 18 SER A 38 1 21 HELIX 3 AA3 ASP A 45 ALA A 60 1 16 HELIX 4 AA4 LYS A 69 GLN A 89 1 21 LINK O3' GNG B 96 P DT B 97 1555 1555 1.61 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