HEADER TRANSFERASE 15-JUN-18 6GT7 TITLE NMR STRUCTURE OF THE FREE HELIX BUNDLE DOMAIN FROM THE FUNCTIONAL PRN1 TITLE 2 PRIMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUNCTIONAL PRN1 PRIMASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HELIX BUNDLE DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS ISLANDICUS; SOURCE 3 ORGANISM_TAXID: 43080; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS FUNCTIONAL PRN1 PRIMASE, REPLICATION INITIATION, DINUCLEOTIDE KEYWDS 2 FORMATION, UNUSUAL ARCHAEO-EUKARYOTIC PRIMASE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.BOUDET,G.LIPPS,F.ALLAIN REVDAT 5 14-JUN-23 6GT7 1 REMARK REVDAT 4 08-MAY-19 6GT7 1 REMARK REVDAT 3 23-JAN-19 6GT7 1 JRNL REVDAT 2 09-JAN-19 6GT7 1 JRNL REVDAT 1 26-DEC-18 6GT7 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: SIMULATED ANNEALING IN IMPLICIT WATER REMARK 3 UNDER FF12SB FORCE-FIELD REMARK 4 REMARK 4 6GT7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010485. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50MM NACL REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-99% 13C; U-99% 15N] REMARK 210 HELIX BUNDLE DOMAIN, 0.9 MM [U- REMARK 210 99% 15N] HELIX BUNDLE DOMAIN, 90% REMARK 210 H2O/10% D2O; 0.7 MM [U-100% 13C] REMARK 210 HELIX BUNDLE DOMAIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-NOESY-HSQC; 13CALI-NOESY REMARK 210 -HSQC; 13CARO-NOESY-HSQC; 13CALI- REMARK 210 HSQC; 13CARO-HSQC; 15N-HSQC; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HN(CO) REMARK 210 CA 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 : CYANA, SPARKY, CANDID REMARK 210 METHOD USED : SIMULATED ANNEALING WITH THE REMARK 210 SANDER MODULE OF AMBER12 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 STRUCTURES FOR LOWEST 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 326 -5.82 -141.61 REMARK 500 1 ASN A 344 -168.96 -162.11 REMARK 500 1 GLU A 345 28.89 -74.11 REMARK 500 1 LYS A 346 -64.77 63.83 REMARK 500 2 ASN A 344 51.43 -158.62 REMARK 500 2 GLU A 345 136.16 62.68 REMARK 500 3 PRO A 289 16.27 -62.01 REMARK 500 3 ASN A 299 18.02 57.22 REMARK 500 3 LYS A 300 -167.52 -79.55 REMARK 500 4 LYS A 300 -168.73 -78.40 REMARK 500 4 ASN A 344 -163.69 -164.24 REMARK 500 4 GLU A 345 35.79 -73.69 REMARK 500 4 LYS A 346 -71.87 61.61 REMARK 500 5 PRO A 289 152.40 -49.41 REMARK 500 5 ASN A 299 17.68 58.67 REMARK 500 5 LYS A 300 -166.68 -79.98 REMARK 500 6 LYS A 286 -157.74 -96.15 REMARK 500 6 SER A 287 76.25 -118.28 REMARK 500 6 LYS A 300 -167.13 -79.26 REMARK 500 6 LYS A 342 -26.28 -143.17 REMARK 500 7 LYS A 342 -34.42 -138.99 REMARK 500 8 ASN A 299 18.77 56.12 REMARK 500 8 LYS A 300 -159.99 -84.52 REMARK 500 8 LYS A 342 -25.80 -143.54 REMARK 500 9 LYS A 342 -29.36 -142.73 REMARK 500 10 ASN A 299 17.28 57.71 REMARK 500 10 THR A 326 -7.34 -140.74 REMARK 500 11 PRO A 289 107.27 -55.92 REMARK 500 11 ASN A 344 -55.77 -163.22 REMARK 500 11 GLU A 345 -122.11 -146.57 REMARK 500 11 LYS A 346 -69.99 -142.47 REMARK 500 12 LYS A 342 -30.27 -139.63 REMARK 500 12 GLU A 343 73.67 -103.53 REMARK 500 13 ASN A 299 27.63 48.26 REMARK 500 13 LYS A 300 -162.18 -79.58 REMARK 500 13 LYS A 342 -28.18 -143.14 REMARK 500 14 LYS A 300 -160.82 -79.17 REMARK 500 14 ASN A 344 -52.58 -162.29 REMARK 500 14 GLU A 345 -89.84 -161.54 REMARK 500 14 LYS A 346 -64.44 -163.20 REMARK 500 15 PRO A 289 29.12 -62.51 REMARK 500 15 LYS A 300 -167.17 -78.88 REMARK 500 15 LYS A 342 -26.87 -142.00 REMARK 500 15 GLU A 345 -80.15 -68.24 REMARK 500 15 LYS A 346 -59.52 -148.45 REMARK 500 16 THR A 326 -8.02 -140.25 REMARK 500 16 LYS A 342 -26.67 -141.19 REMARK 500 17 ASN A 299 17.78 57.11 REMARK 500 17 LYS A 300 -168.90 -78.91 REMARK 500 18 THR A 326 -8.68 -140.89 REMARK 500 REMARK 500 THIS ENTRY HAS 55 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34287 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE FREE HELIX BUNDLE DOMAIN FROM THE FUNCTIONAL REMARK 900 PRN1 PRIMASE DBREF 6GT7 A 256 370 UNP Q54324 Q54324_SULIS 256 370 SEQRES 1 A 115 THR VAL VAL GLU PHE GLU GLU LEU ARG LYS GLU LEU VAL SEQRES 2 A 115 LYS ARG ASP SER GLY LYS PRO VAL GLU LYS ILE LYS GLU SEQRES 3 A 115 GLU ILE CYS THR LYS SER PRO PRO LYS LEU ILE LYS GLU SEQRES 4 A 115 ILE ILE CYS GLU ASN LYS THR TYR ALA ASP VAL ASN ILE SEQRES 5 A 115 ASP ARG SER ARG GLY ASP TRP HIS VAL ILE LEU TYR LEU SEQRES 6 A 115 MET LYS HIS GLY VAL THR ASP PRO ASP LYS ILE LEU GLU SEQRES 7 A 115 LEU LEU PRO ARG ASP SER LYS ALA LYS GLU ASN GLU LYS SEQRES 8 A 115 TRP ASN THR GLN LYS TYR PHE VAL ILE THR LEU SER LYS SEQRES 9 A 115 ALA TRP SER VAL VAL LYS LYS TYR LEU GLU ALA HELIX 1 AA1 THR A 256 ASP A 271 1 16 HELIX 2 AA2 PRO A 275 LYS A 286 1 12 HELIX 3 AA3 LYS A 290 CYS A 297 1 8 HELIX 4 AA4 ASP A 308 GLY A 324 1 17 HELIX 5 AA5 ASP A 327 LEU A 334 1 8 HELIX 6 AA6 LYS A 346 GLU A 369 1 24 SSBOND 1 CYS A 284 CYS A 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