HEADER REPLICATION 06-JAN-23 8FR5 TITLE CRYSTAL STRUCTURE OF THE HUMAN SMACOVIRUS 1 REP DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN SMACOVIRUS 1; SOURCE 3 ORGANISM_TAXID: 1595998; SOURCE 4 STRAIN: FRANCE/2/2008/2548; SOURCE 5 GENE: REP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTD68 KEYWDS DNA BINDING PROTEIN, ENDONUCLEASE, REPLICATION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.K.LIMON,K.SHI,A.DAO,J.RUGLOSKI,K.J.TOMPKINS,H.AIHARA,W.R.GORDON, AUTHOR 2 R.L.EVANS IIII REVDAT 1 27-DEC-23 8FR5 0 JRNL AUTH L.K.LIMON,K.SHI,A.DAO,J.RUGLOSKI,K.J.TOMPKINS,H.AIHARA, JRNL AUTH 2 W.R.GORDON,R.L.EVANS 3RD JRNL TITL THE CRYSTAL STRUCTURE OF THE HUMAN SMACOVIRUS 1 REP DOMAIN. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 79 295 2023 JRNL REFN ESSN 2053-230X JRNL PMID 38051309 JRNL DOI 10.1107/S2053230X23009536 REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 19613 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 3643 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 29.4300 - 3.9400 0.94 1301 145 0.1692 0.2087 REMARK 3 2 3.9400 - 3.1300 0.95 1329 142 0.1781 0.2109 REMARK 3 3 3.1300 - 2.7300 0.95 1338 144 0.1962 0.2355 REMARK 3 4 2.7300 - 2.4800 0.95 1338 150 0.1931 0.1952 REMARK 3 5 2.4800 - 2.3000 0.95 1327 150 0.1998 0.2317 REMARK 3 6 2.3000 - 2.1700 0.93 1290 150 0.1753 0.2216 REMARK 3 7 2.1700 - 2.0600 0.93 1285 139 0.1758 0.1612 REMARK 3 8 2.0600 - 1.9700 0.94 1318 131 0.1676 0.2323 REMARK 3 9 1.9700 - 1.8900 0.95 1334 149 0.1759 0.2741 REMARK 3 10 1.8900 - 1.8300 0.96 1313 143 0.1774 0.1845 REMARK 3 11 1.8300 - 1.7700 0.95 1352 147 0.1694 0.2575 REMARK 3 12 1.7700 - 1.7200 0.95 1318 151 0.1790 0.2134 REMARK 3 13 1.7200 - 1.6800 0.95 1350 149 0.1800 0.2244 REMARK 3 14 1.6800 - 1.6300 0.95 1303 144 0.1779 0.2430 REMARK 3 15 1.6300 - 1.6000 0.95 1329 152 0.1830 0.2349 REMARK 3 16 1.6000 - 1.5600 0.91 1261 141 0.1970 0.2790 REMARK 3 17 1.5600 - 1.5300 0.89 1264 139 0.2266 0.2700 REMARK 3 18 1.5300 - 1.5000 0.90 1224 132 0.2395 0.3096 REMARK 3 19 1.5000 - 1.4800 0.90 1287 138 0.2386 0.3241 REMARK 3 20 1.4800 - 1.4500 0.91 1273 139 0.2325 0.2840 REMARK 3 21 1.4500 - 1.4300 0.89 1196 129 0.2597 0.2969 REMARK 3 22 1.4300 - 1.4100 0.89 1274 147 0.2695 0.2750 REMARK 3 23 1.4100 - 1.3900 0.88 1245 129 0.2994 0.3154 REMARK 3 24 1.3900 - 1.3700 0.87 1202 130 0.3165 0.3606 REMARK 3 25 1.3700 - 1.3500 0.87 1213 144 0.3585 0.4270 REMARK 3 26 1.3500 - 1.3300 0.62 858 89 0.4485 0.4743 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.846 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.77 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 : 0.005 757 REMARK 3 ANGLE : 0.768 1030 REMARK 3 CHIRALITY : 0.079 108 REMARK 3 PLANARITY : 0.006 131 REMARK 3 DIHEDRAL : 18.951 100 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 8FR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000270924. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 29.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04161 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.82190 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.510 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.0, 20% PEG REMARK 280 4000, 1 M GUANIDINE HCL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.68500 REMARK 290 SMTRY3 2 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 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 GLY A 39 REMARK 465 GLU A 40 REMARK 465 ASP A 41 REMARK 465 GLY A 42 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 LYS A 23 CG CD CE NZ REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 ARG A 38 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 43 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 HIS A 70 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 GLU A 85 CG CD OE1 OE2 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 NA A 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 82 O REMARK 620 2 HOH A 235 O 122.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 92 O REMARK 620 2 ASP A 97 OD2 95.4 REMARK 620 N 1 DBREF1 8FR5 A 1 97 UNP A0A0B5CMT4_9VIRU DBREF2 8FR5 A A0A0B5CMT4 1 97 SEQADV 8FR5 PHE A 81 UNP A0A0B5CMT TYR 81 ENGINEERED MUTATION SEQRES 1 A 97 MET THR GLU PRO LYS TRP TYR ASP ILE THR VAL SER LYS SEQRES 2 A 97 ALA LYS CYS PRO GLU GLU ILE LEU ARG LYS TRP LEU ASP SEQRES 3 A 97 GLU ASN GLY GLU ARG TYR ALA TYR GLY ARG GLU ARG GLY SEQRES 4 A 97 GLU ASP GLY TYR GLU HIS PHE GLN VAL ARG VAL VAL LEU SEQRES 5 A 97 ARG ASN PRO THR SER TRP GLU THR MET ARG GLU ILE TRP SEQRES 6 A 97 GLY ASN SER GLY HIS CYS SER PRO THR SER ILE ARG ASN SEQRES 7 A 97 PHE ASP PHE VAL LEU LYS GLU GLY ASP PHE VAL CYS SER SEQRES 8 A 97 TRP ILE LYS VAL PRO ASP HET NA A 101 1 HET NA A 102 1 HET MN A 103 1 HETNAM NA SODIUM ION HETNAM MN MANGANESE (II) ION FORMUL 2 NA 2(NA 1+) FORMUL 4 MN MN 2+ FORMUL 5 HOH *45(H2 O) HELIX 1 AA1 PRO A 17 ASN A 28 1 12 HELIX 2 AA2 SER A 57 GLY A 66 1 10 HELIX 3 AA3 PHE A 79 LYS A 84 5 6 SHEET 1 AA1 5 GLY A 69 PRO A 73 0 SHEET 2 AA1 5 TRP A 6 SER A 12 -1 N ASP A 8 O SER A 72 SHEET 3 AA1 5 HIS A 45 LEU A 52 -1 O VAL A 48 N ILE A 9 SHEET 4 AA1 5 GLY A 29 GLU A 37 -1 N ARG A 31 O VAL A 51 SHEET 5 AA1 5 VAL A 89 CYS A 90 -1 O VAL A 89 N TYR A 34 LINK O VAL A 82 NA NA A 102 1555 1555 2.74 LINK O TRP A 92 NA NA A 101 1555 1555 2.67 LINK OD2 ASP A 97 NA NA A 101 1555 1555 2.65 LINK NA NA A 102 O HOH A 235 1555 1555 3.13 CRYST1 31.160 49.370 31.380 90.00 110.30 90.00 P 1 21 1 2 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 0.032092 0.000000 0.011872 0.00000 SCALE2 0.000000 0.020255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033978 0.00000