HEADER REPLICATION 02-AUG-18 6H8O TITLE CRYSTAL STRUCTURE OF THE MASTER-REP PROTEIN NUCLEASE DOMAIN FROM THE TITLE 2 FABA BEAN NECROTIC YELLOWS VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FABA BEAN NECROTIC YELLOWS VIRUS; SOURCE 3 ORGANISM_TAXID: 59817; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENDONUCLEASE, FABA BEAN NECROTIC YELLOWS VIRUS, REP PROTEIN, DNA KEYWDS 2 REPLICATION, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR G.MONCALIAN,L.GONZALEZ-MONTES REVDAT 2 03-OCT-18 6H8O 1 REMARK SITE ATOM REVDAT 1 22-AUG-18 6H8O 0 JRNL AUTH G.MONCALIAN,L.GONZALEZ-MONTES JRNL TITL CRYSTAL STRUCTURE OF THE MASTER-REP PROTEIN NUCLEASE DOMAIN JRNL TITL 2 FROM THE FABA BEAN NECROTIC YELLOWS VIRUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 81452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4125 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 1.1910 - 1.1500 0.00 0 0 0.2005 0.2052 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6H8O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011184. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99989 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 7.2.2 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81485 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 47.115 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 15.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.11.1_2575 REMARK 200 STARTING MODEL: I3C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 0.1 M SODIUM CITRATE TRIBASIS DIHYDRATE PH5.6, 2.0 REMARK 280 M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.40667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.20333 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 22.80500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.60167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.00833 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 105 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HWT RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE MASTER-REP PROTEIN NUCLEASE DOMAIN (2- REMARK 900 95) FROM THE FABA BEAN NECROTIC YELLOWS VIRUS DBREF1 6H8O A 2 96 UNP A0A2D0XNJ4_9VIRU DBREF2 6H8O A A0A2D0XNJ4 2 96 DBREF1 6H8O B 2 96 UNP A0A2D0XNJ4_9VIRU DBREF2 6H8O B A0A2D0XNJ4 2 96 SEQADV 6H8O LEU A 96 UNP A0A2D0XNJ PHE 96 CONFLICT SEQADV 6H8O LEU B 96 UNP A0A2D0XNJ PHE 96 CONFLICT SEQRES 1 A 95 ALA ARG GLN VAL ILE CYS TRP CYS PHE THR LEU ASN ASN SEQRES 2 A 95 PRO LEU SER PRO LEU SER LEU HIS ASP SER MET LYS TYR SEQRES 3 A 95 LEU VAL TYR GLN THR GLU GLN GLY GLU ALA GLY ASN ILE SEQRES 4 A 95 HIS PHE GLN GLY TYR ILE GLU MET LYS LYS ARG THR SER SEQRES 5 A 95 LEU ALA GLY MET LYS LYS LEU ILE PRO GLY ALA HIS PHE SEQRES 6 A 95 GLU LYS ARG ARG GLY THR GLN GLY GLU ALA ARG ALA TYR SEQRES 7 A 95 SER MET LYS GLU ASP THR ARG LEU GLU GLY PRO TRP GLU SEQRES 8 A 95 TYR GLY GLU LEU SEQRES 1 B 95 ALA ARG GLN VAL ILE CYS TRP CYS PHE THR LEU ASN ASN SEQRES 2 B 95 PRO LEU SER PRO LEU SER LEU HIS ASP SER MET LYS TYR SEQRES 3 B 95 LEU VAL TYR GLN THR GLU GLN GLY GLU ALA GLY ASN ILE SEQRES 4 B 95 HIS PHE GLN GLY TYR ILE GLU MET LYS LYS ARG THR SER SEQRES 5 B 95 LEU ALA GLY MET LYS LYS LEU ILE PRO GLY ALA HIS PHE SEQRES 6 B 95 GLU LYS ARG ARG GLY THR GLN GLY GLU ALA ARG ALA TYR SEQRES 7 B 95 SER MET LYS GLU ASP THR ARG LEU GLU GLY PRO TRP GLU SEQRES 8 B 95 TYR GLY GLU LEU HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 A 103 5 HET SO4 B 101 5 HET SO4 B 102 5 HET SO4 B 103 5 HET SO4 B 104 5 HET SO4 B 105 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 8(O4 S 2-) FORMUL 11 HOH *290(H2 O) HELIX 1 AA1 SER A 53 ILE A 61 1 9 HELIX 2 AA2 THR A 72 SER A 80 1 9 HELIX 3 AA3 SER B 53 ILE B 61 1 9 HELIX 4 AA4 THR B 72 SER B 80 1 9 SHEET 1 AA1 5 ALA A 64 LYS A 68 0 SHEET 2 AA1 5 VAL A 5 ASN A 13 -1 N CYS A 9 O GLU A 67 SHEET 3 AA1 5 ILE A 40 THR A 52 -1 O ILE A 46 N TRP A 8 SHEET 4 AA1 5 MET A 25 GLN A 34 -1 N GLU A 33 O HIS A 41 SHEET 5 AA1 5 ARG A 86 GLY A 94 -1 O LEU A 87 N THR A 32 SHEET 1 AA2 5 ALA B 64 LYS B 68 0 SHEET 2 AA2 5 VAL B 5 ASN B 13 -1 N CYS B 9 O GLU B 67 SHEET 3 AA2 5 ILE B 40 THR B 52 -1 O ILE B 46 N TRP B 8 SHEET 4 AA2 5 MET B 25 GLN B 34 -1 N GLU B 33 O HIS B 41 SHEET 5 AA2 5 ARG B 86 GLY B 94 -1 O LEU B 87 N THR B 32 CISPEP 1 GLY A 89 PRO A 90 0 0.81 CISPEP 2 GLY B 89 PRO B 90 0 1.14 SITE 1 AC1 11 GLY A 35 GLU A 36 HIS A 41 HOH A 211 SITE 2 AC1 11 HOH A 214 HOH A 215 HOH A 220 HOH A 225 SITE 3 AC1 11 HOH A 238 PRO B 62 GLY B 63 SITE 1 AC2 5 VAL A 5 ILE A 6 CYS A 7 HOH A 212 SITE 2 AC2 5 HOH A 242 SITE 1 AC3 4 HIS A 22 ASP A 23 HIS B 22 ASP B 23 SITE 1 AC4 11 PRO A 62 GLY A 63 GLY B 35 GLU B 36 SITE 2 AC4 11 HIS B 41 HOH B 202 HOH B 212 HOH B 225 SITE 3 AC4 11 HOH B 240 HOH B 243 HOH B 247 SITE 1 AC5 6 VAL B 5 ILE B 6 CYS B 7 HOH B 214 SITE 2 AC5 6 HOH B 246 HOH B 272 SITE 1 AC6 4 ARG A 70 ARG B 69 GLY B 71 HOH B 279 SITE 1 AC7 4 ARG A 69 GLY A 71 HOH A 275 ARG B 70 SITE 1 AC8 4 ARG A 70 GLY A 71 ARG B 70 GLY B 71 CRYST1 94.230 94.230 45.610 90.00 90.00 120.00 P 65 12 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 0.010612 0.006127 0.000000 0.00000 SCALE2 0.000000 0.012254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021925 0.00000