HEADER REPLICATION 03-SEP-14 4R94 TITLE STRUCTURE OF THE NICKASE DOMAIN OF NS1 FROM MVM COMPLEXED WITH TITLE 2 MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN NS1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NICKASE DOMAIN (UNP RESIDUES 1-255); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MURINE MINUTE VIRUS; SOURCE 3 ORGANISM_COMMON: MVM; SOURCE 4 ORGANISM_TAXID: 648235; SOURCE 5 STRAIN: MVM PROTOTYPE; SOURCE 6 GENE: NS1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS NICKASE DOMAIN, DNA BINDING, MAGNESIUM, NICKASE, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR L.LIANG,H.ZHAO,L.TANG REVDAT 3 08-NOV-23 4R94 1 REMARK LINK REVDAT 2 22-NOV-17 4R94 1 REMARK REVDAT 1 21-JAN-15 4R94 0 JRNL AUTH S.K.TEWARY,L.LIANG,Z.LIN,A.LYNN,S.F.COTMORE,P.TATTERSALL, JRNL AUTH 2 H.ZHAO,L.TANG JRNL TITL STRUCTURES OF MINUTE VIRUS OF MICE REPLICATION INITIATOR JRNL TITL 2 PROTEIN N-TERMINAL DOMAIN: INSIGHTS INTO DNA NICKING AND JRNL TITL 3 ORIGIN BINDING. JRNL REF VIROLOGY V.476C 61 2014 JRNL REFN ISSN 0042-6822 JRNL PMID 25528417 JRNL DOI 10.1016/J.VIROL.2014.11.022 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 33477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1675 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.6777 - 3.8110 0.98 2850 151 0.1505 0.1990 REMARK 3 2 3.8110 - 3.0285 0.99 2768 144 0.1595 0.2037 REMARK 3 3 3.0285 - 2.6467 0.98 2693 143 0.1959 0.1955 REMARK 3 4 2.6467 - 2.4052 0.98 2679 141 0.1936 0.2316 REMARK 3 5 2.4052 - 2.2330 0.97 2647 139 0.1837 0.2110 REMARK 3 6 2.2330 - 2.1015 0.98 2635 139 0.1814 0.2086 REMARK 3 7 2.1015 - 1.9964 0.97 2612 137 0.1838 0.2351 REMARK 3 8 1.9964 - 1.9096 0.97 2598 138 0.1903 0.2634 REMARK 3 9 1.9096 - 1.8361 0.97 2599 136 0.1939 0.2057 REMARK 3 10 1.8361 - 1.7728 0.96 2600 138 0.2138 0.2303 REMARK 3 11 1.7728 - 1.7174 0.96 2567 134 0.2276 0.2788 REMARK 3 12 1.7174 - 1.6683 0.96 2554 135 0.2120 0.2607 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2130 REMARK 3 ANGLE : 0.971 2878 REMARK 3 CHIRALITY : 0.041 297 REMARK 3 PLANARITY : 0.004 360 REMARK 3 DIHEDRAL : 13.751 773 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4R94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : K-B PAIR OF BIOMORPH MIRRORS REMARK 200 WITH TWO ADDITIONAL HORIZONTALLY REMARK 200 DEFLECTING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.668 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : 0.03600 REMARK 200 FOR THE DATA SET : 37.1180 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.45300 REMARK 200 R SYM FOR SHELL (I) : 0.45300 REMARK 200 FOR SHELL : 3.125 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4PP4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M SODIUM FORMATE, 100MM SODIUM REMARK 280 ACETATE TRIHYDRATE PH 5.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 28.50800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.68850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.50800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.68850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 ASN A 4 REMARK 465 ALA A 5 REMARK 465 ASP A 254 REMARK 465 ASP A 255 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 613 O HOH A 649 1.95 REMARK 500 OE1 GLU A 33 O HOH A 486 2.04 REMARK 500 O HOH A 468 O HOH A 532 2.10 REMARK 500 O HOH A 565 O HOH A 566 2.11 REMARK 500 O HOH A 535 O HOH A 548 2.12 REMARK 500 O HOH A 412 O HOH A 435 2.13 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 SER A 46 30.91 -99.17 REMARK 500 TYR A 210 -63.89 -136.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 119 OE1 REMARK 620 2 HOH A 409 O 82.3 REMARK 620 3 HOH A 421 O 173.4 95.3 REMARK 620 4 HOH A 615 O 89.7 91.9 84.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PP4 RELATED DB: PDB REMARK 900 STRUCTURE OF THE NICKASE DOMAIN OF NS1 FROM MVM REMARK 900 RELATED ID: 3WRN RELATED DB: PDB REMARK 900 STRUCTURE OF THE NICKASE DOMAIN OF NS1 FROM MVM COMPLEXED WITH ZINC DBREF 4R94 A 1 255 UNP P03134 NS1_MUMIP 1 255 SEQRES 1 A 255 MET ALA GLY ASN ALA TYR SER ASP GLU VAL LEU GLY ALA SEQRES 2 A 255 THR ASN TRP LEU LYS GLU LYS SER ASN GLN GLU VAL PHE SEQRES 3 A 255 SER PHE VAL PHE LYS ASN GLU ASN VAL GLN LEU ASN GLY SEQRES 4 A 255 LYS ASP ILE GLY TRP ASN SER TYR LYS LYS GLU LEU GLN SEQRES 5 A 255 GLU ASP GLU LEU LYS SER LEU GLN ARG GLY ALA GLU THR SEQRES 6 A 255 THR TRP ASP GLN SER GLU ASP MET GLU TRP GLU THR THR SEQRES 7 A 255 VAL ASP GLU MET THR LYS LYS GLN VAL PHE ILE PHE ASP SEQRES 8 A 255 SER LEU VAL LYS LYS CYS LEU PHE GLU VAL LEU ASN THR SEQRES 9 A 255 LYS ASN ILE PHE PRO GLY ASP VAL ASN TRP PHE VAL GLN SEQRES 10 A 255 HIS GLU TRP GLY LYS ASP GLN GLY TRP HIS CYS HIS VAL SEQRES 11 A 255 LEU ILE GLY GLY LYS ASP PHE SER GLN ALA GLN GLY LYS SEQRES 12 A 255 TRP TRP ARG ARG GLN LEU ASN VAL TYR TRP SER ARG TRP SEQRES 13 A 255 LEU VAL THR ALA CYS ASN VAL GLN LEU THR PRO ALA GLU SEQRES 14 A 255 ARG ILE LYS LEU ARG GLU ILE ALA GLU ASP ASN GLU TRP SEQRES 15 A 255 VAL THR LEU LEU THR TYR LYS HIS LYS GLN THR LYS LYS SEQRES 16 A 255 ASP TYR THR LYS CYS VAL LEU PHE GLY ASN MET ILE ALA SEQRES 17 A 255 TYR TYR PHE LEU THR LYS LYS LYS ILE SER THR SER PRO SEQRES 18 A 255 PRO ARG ASP GLY GLY TYR PHE LEU SER SER ASP SER GLY SEQRES 19 A 255 TRP LYS THR ASN PHE LEU LYS GLU GLY GLU ARG HIS LEU SEQRES 20 A 255 VAL SER LYS LEU TYR THR ASP ASP HET MG A 301 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *258(H2 O) HELIX 1 1 SER A 7 LYS A 20 1 14 HELIX 2 2 GLU A 53 GLU A 71 1 19 HELIX 3 3 ASP A 80 LYS A 105 1 26 HELIX 4 4 PHE A 108 GLY A 110 5 3 HELIX 5 5 SER A 138 ALA A 140 5 3 HELIX 6 6 GLN A 141 CYS A 161 1 21 HELIX 7 7 THR A 166 ASN A 180 1 15 HELIX 8 8 PHE A 203 TYR A 210 1 8 HELIX 9 9 PHE A 211 LYS A 214 5 4 HELIX 10 10 LYS A 241 THR A 253 1 13 SHEET 1 A 3 VAL A 183 LEU A 185 0 SHEET 2 A 3 GLU A 24 LYS A 31 -1 N VAL A 29 O THR A 184 SHEET 3 A 3 VAL A 201 LEU A 202 -1 O VAL A 201 N VAL A 25 SHEET 1 B 5 VAL A 183 LEU A 185 0 SHEET 2 B 5 GLU A 24 LYS A 31 -1 N VAL A 29 O THR A 184 SHEET 3 B 5 GLY A 125 GLY A 134 -1 O VAL A 130 N PHE A 28 SHEET 4 B 5 VAL A 112 GLY A 121 -1 N ASN A 113 O GLY A 133 SHEET 5 B 5 TYR A 227 ASP A 232 -1 O SER A 231 N VAL A 116 SHEET 1 C 2 VAL A 35 LEU A 37 0 SHEET 2 C 2 LYS A 40 ILE A 42 -1 O ILE A 42 N VAL A 35 LINK OE1 GLU A 119 MG MG A 301 1555 1555 2.07 LINK MG MG A 301 O HOH A 409 1555 1555 2.15 LINK MG MG A 301 O HOH A 421 1555 1555 2.11 LINK MG MG A 301 O HOH A 615 1555 1555 2.05 CISPEP 1 SER A 220 PRO A 221 0 2.13 SITE 1 AC1 6 GLU A 119 HIS A 127 HIS A 129 HOH A 409 SITE 2 AC1 6 HOH A 421 HOH A 615 CRYST1 57.016 121.377 41.581 90.00 90.00 90.00 P 21 21 2 4 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 0.017539 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008239 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024049 0.00000