HEADER VIRAL PROTEIN 03-DEC-18 6IVD TITLE TGEV NSP1 MUTANT - 91-95SG COMPND MOL_ID: 1; COMPND 2 MOLECULE: NSP1 MUTANT PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRANSMISSIBLE GASTROENTERITIS VIRUS; SOURCE 3 ORGANISM_TAXID: 11149; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS TRANSMISSIBLE GASTROENTERITIS VIRUS, NSP1 MUTANT, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.SHEN,G.Q.PENG REVDAT 4 27-MAR-24 6IVD 1 REMARK REVDAT 3 25-SEP-19 6IVD 1 JRNL REVDAT 2 21-AUG-19 6IVD 1 REMARK REVDAT 1 07-AUG-19 6IVD 0 JRNL AUTH Z.SHEN,G.WANG,Y.YANG,J.SHI,L.FANG,F.LI,S.XIAO,Z.F.FU,G.PENG JRNL TITL A CONSERVED REGION OF NONSTRUCTURAL PROTEIN 1 FROM JRNL TITL 2 ALPHACORONAVIRUSES INHIBITS HOST GENE EXPRESSION AND IS JRNL TITL 3 CRITICAL FOR VIRAL VIRULENCE. JRNL REF J.BIOL.CHEM. V. 294 13606 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31350335 JRNL DOI 10.1074/JBC.RA119.009713 REMARK 2 REMARK 2 RESOLUTION. 1.98 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 15284 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 757 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 40.9635 - 3.3759 0.96 2891 175 0.1741 0.2130 REMARK 3 2 3.3759 - 2.6797 0.98 2943 142 0.2074 0.2440 REMARK 3 3 2.6797 - 2.3410 0.98 2906 155 0.2076 0.2792 REMARK 3 4 2.3410 - 2.1270 0.99 2937 136 0.1976 0.2575 REMARK 3 5 2.1270 - 1.9745 0.96 2850 149 0.1935 0.2591 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.55 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 6IVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300010027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-18 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) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15284 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.975 REMARK 200 RESOLUTION RANGE LOW (A) : 40.955 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 2.680 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 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 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM PHOSPHATE DIBASIC, REMARK 280 VAPOR DIFFUSION, SITTING DROP, 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 29.62100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 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 SER A 95 -74.06 -117.07 REMARK 500 SER B 95 -85.29 -114.95 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6IVD A 1 105 UNP A0A140EDJ9_9ALPC DBREF2 6IVD A A0A140EDJ9 1 105 DBREF1 6IVD B 1 105 UNP A0A140EDJ9_9ALPC DBREF2 6IVD B A0A140EDJ9 1 105 SEQADV 6IVD HIS A -1 UNP A0A140EDJ EXPRESSION TAG SEQADV 6IVD HIS A 0 UNP A0A140EDJ EXPRESSION TAG SEQADV 6IVD SER A 91 UNP A0A140EDJ ALA 91 ENGINEERED MUTATION SEQADV 6IVD GLY A 92 UNP A0A140EDJ ASN 92 ENGINEERED MUTATION SEQADV 6IVD SER A 93 UNP A0A140EDJ CYS 93 ENGINEERED MUTATION SEQADV 6IVD GLY A 94 UNP A0A140EDJ ASN 94 ENGINEERED MUTATION SEQADV 6IVD SER A 95 UNP A0A140EDJ GLY 95 ENGINEERED MUTATION SEQADV 6IVD HIS B -1 UNP A0A140EDJ EXPRESSION TAG SEQADV 6IVD HIS B 0 UNP A0A140EDJ EXPRESSION TAG SEQADV 6IVD SER B 91 UNP A0A140EDJ ALA 91 ENGINEERED MUTATION SEQADV 6IVD GLY B 92 UNP A0A140EDJ ASN 92 ENGINEERED MUTATION SEQADV 6IVD SER B 93 UNP A0A140EDJ CYS 93 ENGINEERED MUTATION SEQADV 6IVD GLY B 94 UNP A0A140EDJ ASN 94 ENGINEERED MUTATION SEQADV 6IVD SER B 95 UNP A0A140EDJ GLY 95 ENGINEERED MUTATION SEQRES 1 A 107 HIS HIS MET SER SER LYS GLN PHE LYS ILE LEU VAL ASN SEQRES 2 A 107 GLU ASP TYR GLN VAL ASN VAL PRO SER LEU PRO ILE ARG SEQRES 3 A 107 ASP VAL LEU GLN GLU ILE LYS TYR CYS TYR ARG ASN GLY SEQRES 4 A 107 PHE GLU GLY TYR VAL PHE VAL PRO GLU TYR CYS ARG ASP SEQRES 5 A 107 LEU VAL ASP CYS ASP ARG LYS ASP HIS TYR VAL ILE GLY SEQRES 6 A 107 VAL LEU GLY ASN GLY VAL SER ASP LEU LYS PRO VAL LEU SEQRES 7 A 107 LEU THR GLU PRO SER VAL MET LEU GLN GLY PHE ILE VAL SEQRES 8 A 107 ARG SER GLY SER GLY SER VAL LEU GLU ASP PHE ASP LEU SEQRES 9 A 107 LYS ILE ALA SEQRES 1 B 107 HIS HIS MET SER SER LYS GLN PHE LYS ILE LEU VAL ASN SEQRES 2 B 107 GLU ASP TYR GLN VAL ASN VAL PRO SER LEU PRO ILE ARG SEQRES 3 B 107 ASP VAL LEU GLN GLU ILE LYS TYR CYS TYR ARG ASN GLY SEQRES 4 B 107 PHE GLU GLY TYR VAL PHE VAL PRO GLU TYR CYS ARG ASP SEQRES 5 B 107 LEU VAL ASP CYS ASP ARG LYS ASP HIS TYR VAL ILE GLY SEQRES 6 B 107 VAL LEU GLY ASN GLY VAL SER ASP LEU LYS PRO VAL LEU SEQRES 7 B 107 LEU THR GLU PRO SER VAL MET LEU GLN GLY PHE ILE VAL SEQRES 8 B 107 ARG SER GLY SER GLY SER VAL LEU GLU ASP PHE ASP LEU SEQRES 9 B 107 LYS ILE ALA FORMUL 3 HOH *103(H2 O) HELIX 1 AA1 PRO A 22 GLY A 37 1 16 HELIX 2 AA2 TYR A 47 ASP A 50 5 4 HELIX 3 AA3 PRO B 22 GLY B 37 1 16 HELIX 4 AA4 TYR B 47 ASP B 50 5 4 SHEET 1 AA1 7 LYS A 4 VAL A 10 0 SHEET 2 AA1 7 TYR A 41 PRO A 45 1 O PHE A 43 N LEU A 9 SHEET 3 AA1 7 LEU A 84 ARG A 90 -1 O PHE A 87 N VAL A 44 SHEET 4 AA1 7 VAL A 61 LEU A 65 -1 N VAL A 64 O GLN A 85 SHEET 5 AA1 7 VAL A 69 VAL A 75 -1 O ASP A 71 N LEU A 65 SHEET 6 AA1 7 LEU A 97 ILE A 104 1 O LYS A 103 N LEU A 72 SHEET 7 AA1 7 LYS A 4 VAL A 10 -1 N PHE A 6 O PHE A 100 SHEET 1 AA2 2 VAL A 16 ASN A 17 0 SHEET 2 AA2 2 VAL A 52 ASP A 53 1 O ASP A 53 N VAL A 16 SHEET 1 AA3 7 LYS B 4 VAL B 10 0 SHEET 2 AA3 7 TYR B 41 PRO B 45 1 O PHE B 43 N LEU B 9 SHEET 3 AA3 7 LEU B 84 ARG B 90 -1 O PHE B 87 N VAL B 44 SHEET 4 AA3 7 VAL B 61 LEU B 65 -1 N VAL B 64 O GLN B 85 SHEET 5 AA3 7 SER B 70 VAL B 75 -1 O LYS B 73 N GLY B 63 SHEET 6 AA3 7 LEU B 97 ILE B 104 1 O LYS B 103 N LEU B 72 SHEET 7 AA3 7 LYS B 4 VAL B 10 -1 N PHE B 6 O PHE B 100 SHEET 1 AA4 2 VAL B 16 VAL B 18 0 SHEET 2 AA4 2 VAL B 52 CYS B 54 1 O ASP B 53 N VAL B 18 CRYST1 33.442 59.242 57.175 90.00 97.54 90.00 P 1 21 1 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 0.029903 0.000000 0.003960 0.00000 SCALE2 0.000000 0.016880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017643 0.00000