HEADER VIRAL PROTEIN 17-JUN-22 7Y5M TITLE THE OTU DOMAIN OF TACHENG TICK VIRUS 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: OTU DOMAIN; COMPND 5 SYNONYM: REPLICASE,TRANSCRIPTASE; COMPND 6 EC: 2.7.7.48; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TACHENG TICK VIRUS 1; SOURCE 3 ORGANISM_TAXID: 1608083; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.LI,W.J.WANG,Y.S.XIAO,L.T.SUN REVDAT 3 29-NOV-23 7Y5M 1 REMARK REVDAT 2 15-NOV-23 7Y5M 1 SOURCE REVDAT 1 21-JUN-23 7Y5M 0 JRNL AUTH Z.LI,W.J.WANG,Y.S.XIAO,L.T.SUN JRNL TITL THE OTU DOMAIN OF TACHENG TICK VIRUS 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 26645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1330 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 18.7500 - 3.1200 1.00 3020 156 0.1871 0.2188 REMARK 3 2 3.1200 - 2.4700 1.00 2895 156 0.2058 0.2433 REMARK 3 3 2.4700 - 2.1600 1.00 2849 166 0.1966 0.2220 REMARK 3 4 2.1600 - 1.9700 1.00 2855 133 0.1912 0.2165 REMARK 3 5 1.9700 - 1.8200 0.99 2848 135 0.1926 0.2402 REMARK 3 6 1.8200 - 1.7200 0.99 2783 157 0.2093 0.2286 REMARK 3 7 1.7200 - 1.6300 0.98 2769 143 0.2109 0.2499 REMARK 3 8 1.6300 - 1.5600 0.98 2767 154 0.2141 0.2383 REMARK 3 9 1.5600 - 1.5000 0.91 2529 130 0.2250 0.2805 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) : 0.167 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.901 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.43 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 1270 REMARK 3 ANGLE : 0.895 1730 REMARK 3 CHIRALITY : 0.088 192 REMARK 3 PLANARITY : 0.007 222 REMARK 3 DIHEDRAL : 6.009 166 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): 1.2472 12.8361 -15.7325 REMARK 3 T TENSOR REMARK 3 T11: 0.0967 T22: 0.0797 REMARK 3 T33: 0.0746 T12: -0.0067 REMARK 3 T13: -0.0069 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 1.9575 L22: 1.0720 REMARK 3 L33: 0.9170 L12: -0.2325 REMARK 3 L13: -0.0955 L23: -0.0641 REMARK 3 S TENSOR REMARK 3 S11: 0.0388 S12: -0.0646 S13: -0.0103 REMARK 3 S21: 0.0347 S22: -0.0088 S23: -0.0133 REMARK 3 S31: -0.0193 S32: 0.0217 S33: -0.0265 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 7Y5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-21 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : 27019 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AUTOSOL REMARK 200 STARTING MODEL: 3PHU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000,LITHIUM SULFATE REMARK 280 MONOHYDRATE,MES, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 23.87350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.71000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.71000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.87350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.05500 REMARK 290 SMTRY3 4 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 ALA A 1 REMARK 465 GLY A 2 REMARK 465 ARG A 3 REMARK 465 ARG A 4 REMARK 465 ARG A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 LYS A 163 REMARK 465 GLU A 164 REMARK 465 GLY A 165 REMARK 465 THR A 166 REMARK 465 PRO A 167 REMARK 465 PRO A 168 REMARK 465 ARG A 169 REMARK 465 GLU A 170 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 201 O HOH A 243 2.11 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 CYS A 47 -2.93 85.80 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7Y5M A 1 170 UNP A0A0B5KXW6_9VIRU DBREF2 7Y5M A A0A0B5KXW6 2 171 SEQRES 1 A 170 ALA GLY ARG ARG ARG SER SER ASN LEU SER GLU SER LEU SEQRES 2 A 170 ILE SER ASP CYS ASP ASN LEU GLY ASN PHE TYR ARG GLY SEQRES 3 A 170 PRO ILE VAL LEU ASP ILE ASN LYS GLU PHE THR ILE GLU SEQRES 4 A 170 ASP VAL PRO GLY ASP GLY ASP CYS PHE PHE HIS CYS LEU SEQRES 5 A 170 ALA LYS GLN LEU PRO GLU VAL SER VAL SER ARG LEU LYS SEQRES 6 A 170 GLY ILE ILE THR SER TYR ALA LEU ARG ASN TRP ASP THR SEQRES 7 A 170 LEU THR GLU ALA PRO ARG PHE TYR SER ASP PRO LYS ASP SEQRES 8 A 170 TYR GLU ARG GLU LEU ASN ARG ALA GLY TYR TRP GLY GLY SEQRES 9 A 170 THR THR GLU ALA GLU ILE ILE ASN HIS SER PHE GLY VAL SEQRES 10 A 170 PRO VAL VAL ILE TRP THR THR GLU ASP LYS LYS LEU THR SEQRES 11 A 170 SER ALA VAL GLN VAL TRP THR ARG LYS HIS GLY ASN LEU SEQRES 12 A 170 PRO GLU LEU HIS LEU LEU HIS THR GLY THR HIS PHE MET SEQRES 13 A 170 CYS LEU ALA PRO ILE VAL LYS GLU GLY THR PRO PRO ARG SEQRES 14 A 170 GLU FORMUL 2 HOH *136(H2 O) HELIX 1 AA1 LEU A 9 ILE A 14 1 6 HELIX 2 AA2 SER A 15 CYS A 17 5 3 HELIX 3 AA3 ASP A 31 GLU A 35 1 5 HELIX 4 AA4 CYS A 47 LEU A 56 1 10 HELIX 5 AA5 SER A 60 TRP A 76 1 17 HELIX 6 AA6 ASP A 77 LEU A 79 5 3 HELIX 7 AA7 THR A 80 TYR A 86 1 7 HELIX 8 AA8 ASP A 88 ASN A 97 1 10 HELIX 9 AA9 GLY A 104 GLY A 116 1 13 SHEET 1 AA1 7 ASP A 18 ASN A 19 0 SHEET 2 AA1 7 TYR A 24 GLY A 26 -1 O ARG A 25 N ASP A 18 SHEET 3 AA1 7 ALA A 132 TRP A 136 -1 O VAL A 135 N TYR A 24 SHEET 4 AA1 7 VAL A 119 THR A 124 -1 N ILE A 121 O GLN A 134 SHEET 5 AA1 7 LEU A 146 THR A 151 1 O HIS A 150 N TRP A 122 SHEET 6 AA1 7 HIS A 154 PRO A 160 -1 O HIS A 154 N THR A 151 SHEET 7 AA1 7 PHE A 36 GLU A 39 -1 N THR A 37 O ALA A 159 CRYST1 47.747 58.110 59.420 90.00 90.00 90.00 P 21 21 21 4 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 0.020944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017209 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016829 0.00000 MASTER 260 0 0 9 7 0 0 6 1373 1 0 14 END