HEADER REPLICATION 22-JUL-25 9PQF TITLE XRAY CRYSTAL STRUCTURE OF VIENTOVIRUS FB REP ENDONUCLEASE DOMAIN 2-114 TITLE 2 WITH MG2+ ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP-DEPENDENT HELICASE REP,REPP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN LUNG-ASSOCIATED VIENTOVIRUS FB; SOURCE 3 ORGANISM_TAXID: 2571082; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENDONUCLEASE, DNA BINDING PROTEIN, REPLICATION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.MONTERMOSO,K.GUPTA,R.A.PUMROY,V.MOISEENKOVA-BELL,F.D.BUSHMAN, AUTHOR 2 G.D.VAN DUYNE REVDAT 1 25-FEB-26 9PQF 0 JRNL AUTH S.MONTERMOSO,K.GUPTA,R.A.PUMROY,V.MOISEENKOVA-BELL, JRNL AUTH 2 F.D.BUSHMAN,G.D.VAN DUYNE JRNL TITL STRUCTURES OF NUCLEOTIDE-BOUND REDONDOVIRUS REP PROTEIN LINK JRNL TITL 2 CONFORMATION AND FUNCTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21-5207 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 982 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 45.1300 - 3.4400 1.00 1349 158 0.1605 0.1862 REMARK 3 2 3.4400 - 2.7300 1.00 1296 140 0.1849 0.2098 REMARK 3 3 2.7300 - 2.3900 1.00 1311 106 0.1870 0.2123 REMARK 3 4 2.3900 - 2.1700 1.00 1281 130 0.1797 0.2438 REMARK 3 5 2.1700 - 2.0100 1.00 1275 136 0.1901 0.2527 REMARK 3 6 2.0100 - 1.8900 1.00 1239 153 0.1997 0.2786 REMARK 3 7 1.8900 - 1.8000 1.00 1237 159 0.2460 0.2920 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.91 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 : 0.007 922 REMARK 3 ANGLE : 0.900 1246 REMARK 3 CHIRALITY : 0.061 147 REMARK 3 PLANARITY : 0.006 160 REMARK 3 DIHEDRAL : 13.949 348 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 9PQF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000298035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920100 REMARK 200 MONOCHROMATOR : SI(111) DCM REMARK 200 OPTICS : KB BIMORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS DEV20231129 REMARK 200 DATA SCALING SOFTWARE : DIALS DEV20231129 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.19400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM AMMONIUM MALONATE PH 5.8, 200 REMARK 280 MM POTASSIUM FLUORIDE, 15% W/V PEG 4000, 15% V/V ETHYLENE GLYCOL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 25.47200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.48700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.35250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.47200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.48700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.35250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.47200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.48700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.35250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.47200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.48700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.35250 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 301 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 332 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 347 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 320 O HOH A 330 4555 1.69 REMARK 500 O HOH A 349 O HOH A 349 4565 1.81 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 LEU A 3 108.79 73.24 REMARK 500 GLN A 6 66.52 -157.08 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 48 OE1 REMARK 620 2 HIS A 57 ND1 103.0 REMARK 620 3 HIS A 59 NE2 92.2 112.0 REMARK 620 4 MLI A 202 O6 88.8 93.5 153.5 REMARK 620 5 MLI A 202 O8 168.7 86.3 90.2 84.1 REMARK 620 N 1 2 3 4 DBREF1 9PQF A 2 114 UNP A0A4D6K5Y8_9VIRU DBREF2 9PQF A A0A4D6K5Y8 2 114 SEQADV 9PQF SER A 2 UNP A0A4D6K5Y THR 2 ENGINEERED MUTATION SEQRES 1 A 113 SER LEU ARG LEU GLN ASN LYS ASN LEU TYR LEU THR TYR SEQRES 2 A 113 LEU ASP THR GLU GLU ARG ILE PHE SER GLU LEU ILE LEU SEQRES 3 A 113 ILE THR GLU LEU ALA GLU ARG LEU ASP LYS TYR GLY VAL SEQRES 4 A 113 LYS TYR ALA ILE ALA CYS LYS GLU VAL ALA PRO SER THR SEQRES 5 A 113 GLY THR VAL HIS TYR HIS CYS LEU ILE CYS CYS GLU ASN SEQRES 6 A 113 VAL ILE SER THR ARG ASN GLY LYS GLU LEU LEU THR ILE SEQRES 7 A 113 GLU ASN ILE MET PRO HIS VAL GLY ARG ILE GLN ASN ASN SEQRES 8 A 113 LEU VAL ASN ILE VAL ASN TYR ILE LYS LYS ASP GLY SER SEQRES 9 A 113 PHE ALA GLU VAL ASN LYS GLU ASN ALA HET MG A 201 1 HET MLI A 202 7 HETNAM MG MAGNESIUM ION HETNAM MLI MALONATE ION FORMUL 2 MG MG 2+ FORMUL 3 MLI C3 H2 O4 2- FORMUL 4 HOH *49(H2 O) HELIX 1 AA1 SER A 23 ASP A 36 1 14 HELIX 2 AA2 ASN A 72 THR A 78 1 7 HELIX 3 AA3 ASN A 92 LYS A 102 1 11 SHEET 1 AA1 5 HIS A 85 GLY A 87 0 SHEET 2 AA1 5 LEU A 5 ASP A 16 -1 N THR A 13 O HIS A 85 SHEET 3 AA1 5 VAL A 56 THR A 70 -1 O CYS A 60 N LEU A 12 SHEET 4 AA1 5 VAL A 40 VAL A 49 -1 N LYS A 41 O CYS A 63 SHEET 5 AA1 5 ALA A 107 ASN A 110 -1 O VAL A 109 N ALA A 43 LINK OE1 GLU A 48 MG MG A 201 1555 1555 1.84 LINK ND1 HIS A 57 MG MG A 201 1555 1555 2.72 LINK NE2 HIS A 59 MG MG A 201 1555 1555 2.01 LINK MG MG A 201 O6 MLI A 202 1555 1555 1.88 LINK MG MG A 201 O8 MLI A 202 1555 1555 2.09 CRYST1 50.944 62.974 64.705 90.00 90.00 90.00 I 2 2 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 0.019629 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015455 0.00000 CONECT 391 906 CONECT 449 906 CONECT 474 906 CONECT 906 391 449 474 910 CONECT 906 912 CONECT 907 908 909 CONECT 908 907 910 911 CONECT 909 907 912 913 CONECT 910 906 908 CONECT 911 908 CONECT 912 906 909 CONECT 913 909 MASTER 280 0 2 3 5 0 0 6 961 1 12 9 END