HEADER REPLICATION 05-AUG-19 6Q1M TITLE CRYSTAL STRUCTURE OF THE WHEAT DWARF VIRUS REP DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: REP; COMPND 5 EC: 3.1.21.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: WHEAT DWARF VIRUS; SOURCE 3 ORGANISM_TAXID: 10834; SOURCE 4 GENE: REPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PTD68 KEYWDS HUH-TAG, HUH MOTIF, REP DOMAIN, VIRAL PROTEIN, SINGLE STRANDED DNA, KEYWDS 2 SSDNA, SSDNA BINDING, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR L.A.LITZAU,B.A.EVERETT,R.L.EVANS III,K.SHI,K.TOMPKINS,W.R.GORDON REVDAT 4 11-OCT-23 6Q1M 1 REMARK REVDAT 3 29-APR-20 6Q1M 1 JRNL REVDAT 2 01-JAN-20 6Q1M 1 REMARK REVDAT 1 11-DEC-19 6Q1M 0 JRNL AUTH B.A.EVERETT,L.A.LITZAU,K.TOMPKINS,K.SHI,A.NELSON,H.AIHARA, JRNL AUTH 2 R.L.EVANS III,W.R.GORDON JRNL TITL CRYSTAL STRUCTURE OF THE WHEAT DWARF VIRUS REP DOMAIN. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 75 744 2019 JRNL REFN ESSN 2053-230X JRNL PMID 31797816 JRNL DOI 10.1107/S2053230X19015796 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 51966 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2557 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 46.9200 - 3.2500 0.95 2871 176 0.1744 0.1595 REMARK 3 2 3.2500 - 2.5800 0.98 2808 145 0.1692 0.1759 REMARK 3 3 2.5800 - 2.2500 0.97 2734 138 0.1652 0.1694 REMARK 3 4 2.2500 - 2.0500 0.99 2796 144 0.1460 0.1766 REMARK 3 5 2.0500 - 1.9000 1.00 2765 149 0.1385 0.1637 REMARK 3 6 1.9000 - 1.7900 1.00 2768 150 0.1335 0.1500 REMARK 3 7 1.7900 - 1.7000 0.97 2686 150 0.1269 0.1222 REMARK 3 8 1.7000 - 1.6200 1.00 2755 151 0.1213 0.1427 REMARK 3 9 1.6200 - 1.5600 1.00 2737 133 0.1156 0.1388 REMARK 3 10 1.5600 - 1.5100 1.00 2746 142 0.1175 0.1419 REMARK 3 11 1.5100 - 1.4600 1.00 2734 144 0.1234 0.1473 REMARK 3 12 1.4600 - 1.4200 1.00 2740 135 0.1478 0.1699 REMARK 3 13 1.4200 - 1.3800 0.97 2653 131 0.1922 0.2110 REMARK 3 14 1.3800 - 1.3500 1.00 2733 133 0.1861 0.2319 REMARK 3 15 1.3500 - 1.3200 1.00 2729 132 0.2017 0.2324 REMARK 3 16 1.3200 - 1.2900 1.00 2742 136 0.2139 0.2123 REMARK 3 17 1.2900 - 1.2600 1.00 2745 121 0.2293 0.2589 REMARK 3 18 1.2600 - 1.2400 0.99 2667 147 0.2660 0.3061 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) : 0.112 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.703 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.54 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 : 0.006 1122 REMARK 3 ANGLE : 0.870 1541 REMARK 3 CHIRALITY : 0.086 169 REMARK 3 PLANARITY : 0.006 203 REMARK 3 DIHEDRAL : 12.994 620 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 6Q1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000242510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : .97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52013 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 49.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.95200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: C-ALPHAS OF A TRIMMED PDB ID 1L2M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 72.82650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.78300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.78300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.41325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.78300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.78300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 109.23975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.78300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.78300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.41325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.78300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.78300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 109.23975 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 72.82650 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 0 REMARK 465 SER A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 PRO A 5 REMARK 465 ARG A 6 REMARK 465 THR A 126 REMARK 465 PRO A 127 REMARK 465 GLY A 128 REMARK 465 ARG A 129 REMARK 465 LYS A 130 REMARK 465 ASP A 131 REMARK 465 ARG A 132 REMARK 465 ASP A 133 REMARK 465 ALA A 134 REMARK 465 ASP A 135 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 65 CE NZ 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 GLU A 40 72.70 60.19 REMARK 500 GLU A 40 80.80 42.91 REMARK 500 LYS A 107 -49.32 -133.46 REMARK 500 LYS A 107 -39.89 -137.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 DBREF 6Q1M A -1 135 UNP A7KQY4 A7KQY4_9GEMI 1 137 SEQRES 1 A 137 MET ALA SER SER SER THR PRO ARG PHE ARG VAL TYR SER SEQRES 2 A 137 LYS TYR LEU PHE LEU THR TYR PRO GLN CYS THR LEU GLU SEQRES 3 A 137 PRO GLN TYR ALA LEU ASP SER LEU ARG THR LEU LEU ASN SEQRES 4 A 137 LYS TYR GLU PRO LEU TYR ILE ALA ALA VAL ARG GLU LEU SEQRES 5 A 137 HIS GLU ASP GLY SER PRO HIS LEU HIS VAL LEU VAL GLN SEQRES 6 A 137 ASN LYS LEU ARG ALA SER ILE THR ASN PRO ASN ALA LEU SEQRES 7 A 137 ASN LEU ARG MET ASP THR SER PRO PHE SER ILE PHE HIS SEQRES 8 A 137 PRO ASN ILE GLN ALA ALA LYS ASP CYS ASN GLN VAL ARG SEQRES 9 A 137 ASP TYR ILE THR LYS GLU VAL ASP SER ASP VAL ASN THR SEQRES 10 A 137 ALA GLU TRP GLY THR PHE VAL ALA VAL SER THR PRO GLY SEQRES 11 A 137 ARG LYS ASP ARG ASP ALA ASP HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 HOH *109(H2 O) HELIX 1 AA1 GLU A 24 LEU A 36 1 13 HELIX 2 AA2 ASN A 37 TYR A 39 5 3 HELIX 3 AA3 ASP A 97 LYS A 107 1 11 SHEET 1 AA1 5 ASN A 91 ALA A 94 0 SHEET 2 AA1 5 VAL A 9 PRO A 19 -1 N PHE A 15 O GLN A 93 SHEET 3 AA1 5 PRO A 56 ILE A 70 -1 O LEU A 58 N TYR A 18 SHEET 4 AA1 5 PRO A 41 LEU A 50 -1 N LEU A 42 O GLN A 63 SHEET 5 AA1 5 ALA A 116 GLY A 119 -1 O ALA A 116 N ALA A 46 SHEET 1 AA2 2 LEU A 78 ARG A 79 0 SHEET 2 AA2 2 ILE A 87 PHE A 88 -1 O PHE A 88 N LEU A 78 CISPEP 1 SER A 83 PRO A 84 0 7.14 SITE 1 AC1 8 ALA A 75 ASN A 77 GLU A 117 GLY A 119 SITE 2 AC1 8 THR A 120 PHE A 121 HOH A 328 HOH A 338 SITE 1 AC2 6 TYR A 10 SER A 11 LYS A 12 GLU A 52 SITE 2 AC2 6 ARG A 67 HOH A 334 SITE 1 AC3 7 PHE A 15 GLN A 100 VAL A 101 TYR A 104 SITE 2 AC3 7 GOL A 204 HOH A 351 HOH A 366 SITE 1 AC4 8 GLN A 93 ALA A 94 ALA A 95 LYS A 96 SITE 2 AC4 8 VAL A 101 GOL A 203 HOH A 343 HOH A 366 CRYST1 49.566 49.566 145.653 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 0.020175 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006866 0.00000