HEADER DNA BINDING PROTEIN 21-JUN-18 6GVU TITLE NMR STRUCTURE OF THE DNA-BOUND HELIX BUNDLE DOMAIN FROM THE FUNCTIONAL TITLE 2 PRN1 PRIMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DNA TEMPLATE OF THE PRN1 PRIMASE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FUNCTIONAL PRN1 PRIMASE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: HELIX BUNDLE DOMAIN OF THE FUNCTIONAL PRN1 PRIMASE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SULFOLOBUS ISLANDICUS; SOURCE 4 ORGANISM_TAXID: 43080; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SULFOLOBUS ISLANDICUS; SOURCE 7 ORGANISM_TAXID: 43080; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PRIMASE, SINGLE-STRANDED DNA, REPLICATION INITIATION, DNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.BOUDET,G.LIPPS,F.H.-T.ALLAIN REVDAT 5 14-JUN-23 6GVU 1 REMARK REVDAT 4 08-MAY-19 6GVU 1 REMARK REVDAT 3 23-JAN-19 6GVU 1 JRNL REVDAT 2 09-JAN-19 6GVU 1 JRNL REVDAT 1 26-DEC-18 6GVU 0 JRNL AUTH J.BOUDET,J.C.DEVILLIER,T.WIEGAND,L.SALMON,B.H.MEIER,G.LIPPS, JRNL AUTH 2 F.H.ALLAIN JRNL TITL A SMALL HELICAL BUNDLE PREPARES PRIMER SYNTHESIS BY BINDING JRNL TITL 2 TWO NUCLEOTIDES THAT ENHANCE SEQUENCE-SPECIFIC RECOGNITION JRNL TITL 3 OF THE DNA TEMPLATE. JRNL REF CELL V. 176 154 2019 JRNL REFN ISSN 1097-4172 JRNL PMID 30595448 JRNL DOI 10.1016/J.CELL.2018.11.031 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 6GVU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010607. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323; 298; 298 REMARK 210 PH : 5.5; 5.5; 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL; 100MM NACL; 50MM REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM; REMARK 210 AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 DNA-BOUND HELIX BUNDLE DOMAIN, 1.0 MM DNA (5'-D(*CP*TP*GP*TP*GP* REMARK 210 CP*TP*CP*A)-3'), 90% H2O/10% D2O; 0.7 MM [U-100% 13C] DNA-BOUND REMARK 210 HELIX BUNDLE DOMAIN, 0.7 MM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A) REMARK 210 -3'), 100% D2O; 1.1 MM [U-99% 15N] DNA-BOUND HELIX BUNDLE DOMAIN, REMARK 210 1.1 MM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 90% H2O/10% REMARK 210 D2O; 1.0 MM DNA-BOUND HELIX BUNDLE DOMAIN, 1.0 MM DNA (5'-D(*CP* REMARK 210 TP*GP*TP*GP*CP*TP*CP*A)-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 H(CCO)NH; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 2D 1H-15N HSQC; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D-F1FF2F-NOESY; 2D-F2F-NOESY; REMARK 210 3D 13C-ALIPHATIC HFILTERED- REMARK 210 HEDITED NOESY; 3D 13C-AROMATIC REMARK 210 HFILTERED-HEDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, CANDID, TOPSPIN, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 5 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 5 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 5 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 6 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 6 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 6 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 172 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 1 ASN B 344 16.04 53.08 REMARK 500 2 ASP B 327 113.87 -163.42 REMARK 500 2 LEU B 335 73.74 39.98 REMARK 500 2 LYS B 342 23.24 -150.82 REMARK 500 3 ASP B 327 122.08 -171.04 REMARK 500 4 LYS B 286 -157.59 -88.55 REMARK 500 4 ASP B 327 118.21 -170.69 REMARK 500 5 SER B 287 73.20 52.51 REMARK 500 5 ASP B 327 114.65 -162.64 REMARK 500 5 LYS B 346 -156.79 -165.82 REMARK 500 6 ASP B 327 120.32 -171.64 REMARK 500 7 ASN B 344 15.41 53.34 REMARK 500 8 ASP B 327 119.79 -166.28 REMARK 500 8 LYS B 342 24.27 -152.36 REMARK 500 9 LYS B 342 15.32 -147.71 REMARK 500 10 SER B 287 76.00 52.83 REMARK 500 10 PRO B 288 170.09 -59.24 REMARK 500 10 ASP B 327 122.80 -171.42 REMARK 500 11 SER B 287 78.45 -111.76 REMARK 500 12 LEU B 335 58.57 32.95 REMARK 500 12 ASN B 344 19.57 53.02 REMARK 500 13 SER B 287 72.76 52.17 REMARK 500 13 HIS B 323 0.61 -68.80 REMARK 500 13 ASP B 327 117.81 -167.78 REMARK 500 16 ASP B 327 116.90 -168.85 REMARK 500 16 ASP B 338 30.21 -145.41 REMARK 500 17 ASP B 327 119.60 -168.11 REMARK 500 17 ASN B 344 29.17 44.52 REMARK 500 17 LYS B 346 -169.69 -163.69 REMARK 500 18 HIS B 323 1.40 -68.47 REMARK 500 18 ASN B 344 28.31 42.61 REMARK 500 19 ASP B 327 119.18 -168.98 REMARK 500 19 LYS B 342 19.11 -147.41 REMARK 500 20 LYS B 286 -158.55 -84.61 REMARK 500 20 ASN B 344 18.59 52.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34291 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE DNA-BOUND HELIX BUNDLE DOMAIN FROM THE REMARK 900 FUNCTIONAL PRN1 PRIMASE DBREF 6GVU A 1 9 PDB 6GVU 6GVU 1 9 DBREF 6GVU B 256 370 UNP Q54324 Q54324_SULIS 256 370 SEQRES 1 A 9 DC DT DG DT DG DC DT DC DA SEQRES 1 B 115 THR VAL VAL GLU PHE GLU GLU LEU ARG LYS GLU LEU VAL SEQRES 2 B 115 LYS ARG ASP SER GLY LYS PRO VAL GLU LYS ILE LYS GLU SEQRES 3 B 115 GLU ILE CYS THR LYS SER PRO PRO LYS LEU ILE LYS GLU SEQRES 4 B 115 ILE ILE CYS GLU ASN LYS THR TYR ALA ASP VAL ASN ILE SEQRES 5 B 115 ASP ARG SER ARG GLY ASP TRP HIS VAL ILE LEU TYR LEU SEQRES 6 B 115 MET LYS HIS GLY VAL THR ASP PRO ASP LYS ILE LEU GLU SEQRES 7 B 115 LEU LEU PRO ARG ASP SER LYS ALA LYS GLU ASN GLU LYS SEQRES 8 B 115 TRP ASN THR GLN LYS TYR PHE VAL ILE THR LEU SER LYS SEQRES 9 B 115 ALA TRP SER VAL VAL LYS LYS TYR LEU GLU ALA HELIX 1 AA1 THR B 256 ARG B 270 1 15 HELIX 2 AA2 PRO B 275 THR B 285 1 11 HELIX 3 AA3 PRO B 289 ILE B 296 1 8 HELIX 4 AA4 THR B 301 ASN B 306 1 6 HELIX 5 AA5 ASP B 308 HIS B 323 1 16 HELIX 6 AA6 ASP B 327 LEU B 334 1 8 HELIX 7 AA7 TRP B 347 GLU B 369 1 23 SSBOND 1 CYS B 284 CYS B 297 1555 1555 2.04 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