HEADER VIRAL PROTEIN 29-NOV-21 7SZY TITLE HIGH-RESOLUTION STRUCTURE OF THE NUCLEASE DOMAIN FROM THE MAIN TITLE 2 REPLICATION PROTEIN NS1 OF HUMAN PARVOVIRUS B19 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN PARVOVIRUS B19; SOURCE 3 ORGANISM_TAXID: 10798; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEASE DOMAIN, VIRAL ORIGIN OF REPLICATION BINDING DOMAIN, KEYWDS 2 PARVOVIRUS, DOUBLE-STRANDED DNA BINDING, DNA NICKING, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.C.HORTON REVDAT 4 18-OCT-23 7SZY 1 REMARK REVDAT 3 25-MAY-22 7SZY 1 JRNL REVDAT 2 04-MAY-22 7SZY 1 JRNL REVDAT 1 30-MAR-22 7SZY 0 JRNL AUTH J.L.SANCHEZ,N.GHADIRIAN,N.C.HORTON JRNL TITL HIGH-RESOLUTION STRUCTURE OF THE NUCLEASE DOMAIN OF THE JRNL TITL 2 HUMAN PARVOVIRUS B19 MAIN REPLICATION PROTEIN NS1. JRNL REF J.VIROL. V. 96 16421 2022 JRNL REFN ESSN 1098-5514 JRNL PMID 35435730 JRNL DOI 10.1128/JVI.02164-21 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4080 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 6797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 333 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 45.0600 - 3.0200 0.99 3305 167 0.1805 0.2379 REMARK 3 2 3.0200 - 2.4000 0.98 3159 166 0.2391 0.2969 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) : 0.278 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.11 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 : 0.003 1382 REMARK 3 ANGLE : 0.613 1881 REMARK 3 CHIRALITY : 0.041 210 REMARK 3 PLANARITY : 0.003 239 REMARK 3 DIHEDRAL : 19.483 473 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 7SZY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000259606. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6799 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.10220 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53310 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.430 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6USM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350 0.1M SODIUM CITRATE PH REMARK 280 4.5 0.1M NACL 0.1M LICL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.49500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.49500 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 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 GLY A 1 REMARK 465 ALA A 176 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 ASN A 13 CG OD1 ND2 REMARK 470 PHE A 57 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR A 58 OG1 REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 ARG A 94 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 LYS A 129 CG CD CE NZ REMARK 470 GLN A 136 NE2 REMARK 470 GLU A 139 CD OE1 OE2 REMARK 470 ILE A 146 CD1 REMARK 470 ASP A 158 CG OD1 OD2 REMARK 470 HIS A 175 CG ND1 CD2 CE1 NE2 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 ASN A 19 -169.64 -103.34 REMARK 500 CYS A 24 36.18 -83.00 REMARK 500 HIS A 39 -134.76 59.27 REMARK 500 TYR A 141 -59.28 -136.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 389 DISTANCE = 7.07 ANGSTROMS DBREF 7SZY A 2 176 UNP A3F778 A3F778_PAVHB 2 176 SEQADV 7SZY GLY A 1 UNP A3F778 EXPRESSION TAG SEQRES 1 A 176 GLY GLU LEU PHE ARG GLY VAL LEU HIS ILE SER SER ASN SEQRES 2 A 176 ILE LEU ASP CYS ALA ASN ASP ASN TRP TRP CYS SER MET SEQRES 3 A 176 LEU ASP LEU ASP THR SER ASP TRP GLU PRO LEU THR HIS SEQRES 4 A 176 SER ASN ARG LEU MET ALA ILE TYR LEU SER ASN VAL ALA SEQRES 5 A 176 SER ARG LEU ASP PHE THR GLY GLY PRO LEU ALA GLY CYS SEQRES 6 A 176 LEU TYR PHE PHE GLN VAL GLU CYS ASN LYS PHE GLU GLU SEQRES 7 A 176 GLY TYR HIS ILE HIS VAL VAL ILE GLY GLY PRO GLY LEU SEQRES 8 A 176 ASN ALA ARG ASN LEU THR VAL CYS VAL GLU GLY LEU PHE SEQRES 9 A 176 ASN ASN VAL LEU TYR HIS LEU VAL ASN GLU SER VAL LYS SEQRES 10 A 176 LEU LYS PHE LEU PRO GLY MET THR THR LYS GLY LYS TYR SEQRES 11 A 176 PHE ARG ASP GLY GLU GLN PHE ILE GLU ASN TYR LEU MET SEQRES 12 A 176 LYS LYS ILE PRO LEU ASN VAL VAL TRP CYS VAL THR ASN SEQRES 13 A 176 ILE ASP GLY TYR ILE ASP THR CYS ILE SER ALA SER PHE SEQRES 14 A 176 ARG ARG GLY ALA CYS HIS ALA HET CIT A 201 13 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *89(H2 O) HELIX 1 AA1 SER A 11 CYS A 17 1 7 HELIX 2 AA2 ASN A 19 CYS A 24 1 6 HELIX 3 AA3 THR A 38 PHE A 57 1 20 HELIX 4 AA4 GLY A 59 ALA A 63 5 5 HELIX 5 AA5 ASN A 95 HIS A 110 1 16 HELIX 6 AA6 ASP A 133 TYR A 141 1 9 HELIX 7 AA7 LEU A 142 LYS A 145 5 4 HELIX 8 AA8 GLY A 159 CYS A 164 1 6 HELIX 9 AA9 SER A 166 HIS A 175 1 10 SHEET 1 AA1 5 PHE A 120 PRO A 122 0 SHEET 2 AA1 5 PHE A 4 ILE A 10 -1 N VAL A 7 O LEU A 121 SHEET 3 AA1 5 TYR A 80 GLY A 87 -1 O VAL A 84 N GLY A 6 SHEET 4 AA1 5 LEU A 66 CYS A 73 -1 N GLN A 70 O HIS A 83 SHEET 5 AA1 5 VAL A 150 THR A 155 -1 O VAL A 154 N PHE A 69 CISPEP 1 PRO A 147 LEU A 148 0 4.78 CRYST1 45.060 49.100 74.990 90.00 90.00 90.00 P 2 21 21 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 0.022193 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013335 0.00000