HEADER TRANSCRIPTION 16-DEC-09 2KRC TITLE SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF BACILLUS SUBTILIS DELTA TITLE 2 SUBUNIT OF RNA POLYMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED RNA POLYMERASE SUBUNIT DELTA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-92; COMPND 5 SYNONYM: N DELTA, RNAP DELTA FACTOR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET22B KEYWDS RNA POLYMERASE, DELTA SUBUNIT, GRAM-POSITIVE BACTERIA, DNA-DIRECTED KEYWDS 2 RNA POLYMERASE, NUCLEOTIDYLTRANSFERASE, TRANSCRIPTION, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR V.MOTACKOVA,H.SANDEROVA,L.ZIDEK,J.NOVACEK,P.PADRTA,A.SVENKOVA, AUTHOR 2 J.JONAK,L.KRASNY,V.SKLENAR REVDAT 3 16-MAR-22 2KRC 1 REMARK SEQADV REVDAT 2 21-APR-10 2KRC 1 JRNL REVDAT 1 07-APR-10 2KRC 0 JRNL AUTH V.MOTACKOVA,H.SANDEROVA,L.ZIDEK,J.NOVACEK,P.PADRTA, JRNL AUTH 2 A.SVENKOVA,J.KORELUSOVA,J.JONAK,L.KRASNY,V.SKLENAR JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF BACILLUS JRNL TITL 2 SUBTILIS DELTA SUBUNIT OF RNA POLYMERASE AND ITS JRNL TITL 3 CLASSIFICATION BASED ON STRUCTURAL HOMOLOGS JRNL REF PROTEINS V. 78 1807 2010 JRNL REFN ISSN 0887-3585 JRNL PMID 20310067 JRNL DOI 10.1002/PROT.22708 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 3.0, CNS 1.2, X-PLOR REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KRC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000101477. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10 MM SODIUM CHLORIDE-1, 50 UM REMARK 210 SODIUM AZIDE-2, 20 MM PHOSPHATE REMARK 210 BUFFER-3, 90% H2O/10% D2O; 10 MM REMARK 210 SODIUM CHLORIDE-4, 50 UM SODIUM REMARK 210 AZIDE-5, 20 MM PHOSPHATE BUFFER- REMARK 210 6, 14.29 MG/ML FILAMENTOUS PF1 REMARK 210 BACTERIOPHAGE-7, 90% H2O/10% D2O; REMARK 210 10 MM SODIUM CHLORIDE-8, 50 UM REMARK 210 SODIUM AZIDE-9, 20 MM PHOSPHATE REMARK 210 BUFFER-10, 5 % POLYACRYLAMIDE REMARK 210 GEL-11, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HMQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HNCO; 3D HNHA; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; (HB)CB(CGCD)HD; 2D REMARK 210 1H-15N IPAP; 2D HN[C]-S3E; 2D (H) REMARK 210 CACO-IPAP; 2D 13C-COUPLED 1H-13C REMARK 210 HSQC; 2D 13C-DETECTED CON REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW 3.0, SPARKY 3.111, ARIA REMARK 210 2.1, CNS 1.2, S3EPY REMARK 210 METHOD USED : MOLECULAR DYNAMICS, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 HH21 ARG A 67 OE1 GLU A 94 1.58 REMARK 500 HD1 HIS A 21 OE1 GLU A 22 1.59 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 ILE A 3 -96.28 63.72 REMARK 500 1 GLN A 5 21.65 -161.20 REMARK 500 1 PHE A 68 146.27 62.35 REMARK 500 1 LEU A 71 -84.40 -78.06 REMARK 500 1 SER A 72 -61.32 -90.80 REMARK 500 1 ASP A 73 -61.57 -162.03 REMARK 500 1 TYR A 84 -70.27 177.82 REMARK 500 1 ASP A 85 10.75 -147.19 REMARK 500 1 GLN A 86 117.66 -173.48 REMARK 500 1 LEU A 93 89.24 61.38 REMARK 500 1 GLU A 94 105.16 49.77 REMARK 500 1 HIS A 97 74.17 52.45 REMARK 500 1 HIS A 99 -55.89 -156.94 REMARK 500 2 LYS A 4 1.73 -68.03 REMARK 500 2 LEU A 71 -83.24 -76.45 REMARK 500 2 ASP A 73 -52.68 -153.35 REMARK 500 2 ARG A 79 0.16 -63.80 REMARK 500 2 GLU A 90 21.70 -75.90 REMARK 500 2 GLN A 92 -64.63 -126.25 REMARK 500 2 LEU A 93 -153.11 -144.14 REMARK 500 2 HIS A 97 -70.93 70.40 REMARK 500 2 HIS A 98 42.26 -162.26 REMARK 500 2 HIS A 99 -48.00 78.91 REMARK 500 3 ARG A 67 -157.03 -101.18 REMARK 500 3 PHE A 68 107.90 48.80 REMARK 500 3 LEU A 71 -90.12 -98.53 REMARK 500 3 SER A 72 -61.52 -91.38 REMARK 500 3 GLN A 74 -12.03 68.87 REMARK 500 3 TYR A 84 77.35 175.70 REMARK 500 3 ASP A 85 -63.36 64.60 REMARK 500 3 GLN A 86 -70.23 -91.09 REMARK 500 3 LEU A 87 98.40 71.29 REMARK 500 3 ASP A 88 80.42 76.12 REMARK 500 3 LEU A 93 83.20 82.17 REMARK 500 3 GLU A 94 131.24 59.52 REMARK 500 3 HIS A 97 -81.00 67.00 REMARK 500 3 HIS A 98 -178.04 163.73 REMARK 500 4 LYS A 4 15.36 -65.39 REMARK 500 4 LEU A 71 -91.05 -76.75 REMARK 500 4 SER A 72 -60.34 -92.40 REMARK 500 4 ASP A 73 -37.85 -157.44 REMARK 500 4 TYR A 84 84.42 -179.40 REMARK 500 4 ASP A 85 -40.70 70.81 REMARK 500 4 GLN A 92 -62.91 -126.06 REMARK 500 4 LEU A 93 -145.30 -167.94 REMARK 500 4 GLU A 94 69.16 -68.37 REMARK 500 4 HIS A 97 -82.17 56.01 REMARK 500 5 ILE A 3 -82.75 -135.80 REMARK 500 5 GLN A 5 20.16 -158.80 REMARK 500 5 LEU A 71 -80.93 -78.93 REMARK 500 REMARK 500 THIS ENTRY HAS 120 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 ARG A 79 0.09 SIDE CHAIN REMARK 500 4 ARG A 67 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16635 RELATED DB: BMRB DBREF 2KRC A 2 92 UNP P12464 RPOE_BACSU 2 92 SEQADV 2KRC LEU A 93 UNP P12464 EXPRESSION TAG SEQADV 2KRC GLU A 94 UNP P12464 EXPRESSION TAG SEQADV 2KRC HIS A 95 UNP P12464 EXPRESSION TAG SEQADV 2KRC HIS A 96 UNP P12464 EXPRESSION TAG SEQADV 2KRC HIS A 97 UNP P12464 EXPRESSION TAG SEQADV 2KRC HIS A 98 UNP P12464 EXPRESSION TAG SEQADV 2KRC HIS A 99 UNP P12464 EXPRESSION TAG SEQADV 2KRC HIS A 100 UNP P12464 EXPRESSION TAG SEQRES 1 A 99 GLY ILE LYS GLN TYR SER GLN GLU GLU LEU LYS GLU MET SEQRES 2 A 99 ALA LEU VAL GLU ILE ALA HIS GLU LEU PHE GLU GLU HIS SEQRES 3 A 99 LYS LYS PRO VAL PRO PHE GLN GLU LEU LEU ASN GLU ILE SEQRES 4 A 99 ALA SER LEU LEU GLY VAL LYS LYS GLU GLU LEU GLY ASP SEQRES 5 A 99 ARG ILE ALA GLN PHE TYR THR ASP LEU ASN ILE ASP GLY SEQRES 6 A 99 ARG PHE LEU ALA LEU SER ASP GLN THR TRP GLY LEU ARG SEQRES 7 A 99 SER TRP TYR PRO TYR ASP GLN LEU ASP GLU GLU THR GLN SEQRES 8 A 99 LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 SER A 7 GLU A 13 1 7 HELIX 2 2 ALA A 15 LYS A 28 1 14 HELIX 3 3 PHE A 33 GLY A 45 1 13 HELIX 4 4 LYS A 47 LEU A 51 5 5 HELIX 5 5 GLY A 52 ILE A 64 1 13 HELIX 6 6 LEU A 78 TYR A 82 5 5 SHEET 1 A 3 VAL A 31 PRO A 32 0 SHEET 2 A 3 THR A 75 GLY A 77 -1 O TRP A 76 N VAL A 31 SHEET 3 A 3 LEU A 69 ALA A 70 -1 N LEU A 69 O GLY A 77 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