HEADER DNA BINDING PROTEIN 16-JUN-22 7Y56 TITLE CRYSTAL STRUCTURE OF NS1 NUCLEASE DOMAIN IN P41212 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEASE DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN PARVOVIRUS B19; SOURCE 3 ORGANISM_COMMON: HPV B19; SOURCE 4 ORGANISM_TAXID: 10798; SOURCE 5 GENE: NS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NS1, NUCLEASE DOMAIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.Y.ZHANG,J.H.GAN REVDAT 2 13-NOV-24 7Y56 1 REMARK REVDAT 1 05-JUL-23 7Y56 0 JRNL AUTH Y.ZHANG,Z.SHAO,Y.GAO,B.FAN,J.YANG,X.CHEN,X.ZHAO,Q.SHAO, JRNL AUTH 2 W.ZHANG,C.CAO,H.LIU,J.GAN JRNL TITL STRUCTURES AND IMPLICATIONS OF THE NUCLEASE DOMAIN OF HUMAN JRNL TITL 2 PARVOVIRUS B19 NS1 PROTEIN. JRNL REF COMPUT STRUCT BIOTECHNOL J V. 20 4645 2022 JRNL REFN ESSN 2001-0370 JRNL PMID 36090819 JRNL DOI 10.1016/J.CSBJ.2022.08.047 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 27340 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1379 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 30.0000 - 3.7729 0.99 2792 140 0.1775 0.1828 REMARK 3 2 3.7729 - 2.9954 1.00 2654 143 0.1751 0.1961 REMARK 3 3 2.9954 - 2.6169 1.00 2627 139 0.1845 0.1960 REMARK 3 4 2.6169 - 2.3777 1.00 2566 151 0.1805 0.1984 REMARK 3 5 2.3777 - 2.2074 1.00 2597 133 0.1753 0.2036 REMARK 3 6 2.2074 - 2.0772 1.00 2531 157 0.1736 0.2278 REMARK 3 7 2.0772 - 1.9732 1.00 2575 125 0.1827 0.2396 REMARK 3 8 1.9732 - 1.8873 1.00 2579 114 0.1851 0.2051 REMARK 3 9 1.8873 - 1.8147 1.00 2555 131 0.1959 0.2428 REMARK 3 10 1.8147 - 1.7521 0.98 2485 146 0.1961 0.2171 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.38 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 1428 REMARK 3 ANGLE : 0.843 1944 REMARK 3 CHIRALITY : 0.055 217 REMARK 3 PLANARITY : 0.005 247 REMARK 3 DIHEDRAL : 2.535 1140 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 48.9656 31.7331 37.2900 REMARK 3 T TENSOR REMARK 3 T11: 0.1065 T22: 0.1117 REMARK 3 T33: 0.1272 T12: -0.0022 REMARK 3 T13: -0.0027 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 1.2142 L22: 0.8790 REMARK 3 L33: 1.4810 L12: -0.3131 REMARK 3 L13: -0.1510 L23: -0.0082 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: -0.0600 S13: 0.0239 REMARK 3 S21: 0.0598 S22: -0.0177 S23: -0.0510 REMARK 3 S31: -0.0366 S32: 0.1058 S33: 0.0318 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 7Y56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 50954 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM PHOSPHATE (DIBASIC) AND REMARK 280 SODIUM ACETATE/ACETIC ACID PH 4.2 BUFFER, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 54.42800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.68000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.21400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.68000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.68000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.64200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.68000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.68000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.21400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.68000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.68000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 81.64200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.42800 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 469 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 HIS A 175 REMARK 465 ALA A 176 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 HIS A 39 -137.36 51.52 REMARK 500 TYR A 141 -59.05 -132.33 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 484 DISTANCE = 5.86 ANGSTROMS DBREF 7Y56 A 2 176 UNP Q75U85 Q75U85_PAVHB 2 176 SEQADV 7Y56 GLY A 0 UNP Q75U85 EXPRESSION TAG SEQADV 7Y56 SER A 1 UNP Q75U85 EXPRESSION TAG SEQRES 1 A 177 GLY SER GLU LEU PHE ARG GLY VAL LEU GLN VAL SER SER SEQRES 2 A 177 ASN VAL LEU ASP CYS ALA ASN ASP ASN TRP TRP CYS SER SEQRES 3 A 177 LEU LEU ASP LEU ASP THR SER ASP TRP GLU PRO LEU THR SEQRES 4 A 177 HIS THR ASN ARG LEU MSE ALA ILE TYR LEU SER SER VAL SEQRES 5 A 177 ALA SER LYS LEU ASP PHE THR GLY GLY PRO LEU ALA GLY SEQRES 6 A 177 CYS LEU TYR PHE PHE GLN VAL GLU CYS ASN LYS PHE GLU SEQRES 7 A 177 GLU GLY TYR HIS ILE HIS VAL VAL ILE GLY GLY PRO GLY SEQRES 8 A 177 LEU ASN PRO ARG ASN LEU THR VAL CYS VAL GLU GLY LEU SEQRES 9 A 177 PHE ASN ASN VAL LEU TYR HIS LEU VAL THR GLY ASN VAL SEQRES 10 A 177 LYS LEU LYS PHE LEU PRO GLY MSE THR THR LYS GLY LYS SEQRES 11 A 177 TYR PHE ARG ASP GLY GLU GLN PHE ILE GLU ASN TYR LEU SEQRES 12 A 177 MSE LYS LYS ILE PRO LEU ASN VAL VAL TRP CYS VAL THR SEQRES 13 A 177 ASN ILE ASP GLY TYR ILE ASP THR CYS ILE SER ALA THR SEQRES 14 A 177 PHE ARG ARG GLY ALA CYS HIS ALA MODRES 7Y56 MSE A 44 MET MODIFIED RESIDUE MODRES 7Y56 MSE A 124 MET MODIFIED RESIDUE MODRES 7Y56 MSE A 143 MET MODIFIED RESIDUE HET MSE A 44 8 HET MSE A 124 8 HET MSE A 143 8 HET GOL A 201 6 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *184(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 THR A 58 ALA A 63 5 6 HELIX 5 AA5 ASN A 95 TYR A 109 1 15 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 ILE A 157 ILE A 161 5 5 HELIX 9 AA9 SER A 166 CYS A 174 1 9 SHEET 1 AA1 5 PHE A 120 PRO A 122 0 SHEET 2 AA1 5 PHE A 4 VAL 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 GLU A 72 -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 LINK C LEU A 43 N MSE A 44 1555 1555 1.33 LINK C MSE A 44 N ALA A 45 1555 1555 1.33 LINK C GLY A 123 N MSE A 124 1555 1555 1.33 LINK C MSE A 124 N THR A 125 1555 1555 1.33 LINK C LEU A 142 N MSE A 143 1555 1555 1.33 LINK C MSE A 143 N LYS A 144 1555 1555 1.33 CISPEP 1 PRO A 147 LEU A 148 0 1.09 CRYST1 69.360 69.360 108.856 90.00 90.00 90.00 P 41 21 2 8 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 0.014418 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009186 0.00000