HEADER RNA BINDING PROTEIN 21-OCT-17 5YM8 TITLE CRYSTAL STRUCTURE OF PORCINE DELTA CORONAVIRUS NSP9-N7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NSP9; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PEDV MAIN PROTEASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORCINE CORONAVIRUS HKU15; SOURCE 3 ORGANISM_TAXID: 1159905; SOURCE 4 GENE: ORF1AB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PORCINE DELTA CORONAVIRUS, RNA BINDING PROTEIN, NSP9 EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZENG,G.Q.PENG REVDAT 3 27-MAR-24 5YM8 1 REMARK REVDAT 2 03-JUL-19 5YM8 1 JRNL REVDAT 1 13-JUN-18 5YM8 0 JRNL AUTH Z.ZENG,F.DENG,K.SHI,G.YE,G.WANG,L.FANG,S.XIAO,Z.FU,G.PENG JRNL TITL DIMERIZATION OF CORONAVIRUS NSP9 WITH DIVERSE MODES ENHANCES JRNL TITL 2 ITS NUCLEIC ACID BINDING AFFINITY. JRNL REF J.VIROL. V. 92 2018 JRNL REFN ESSN 1098-5514 JRNL PMID 29925659 JRNL DOI 10.1128/JVI.00692-18 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 12364 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 611 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 34.9267 - 3.1622 0.99 2961 158 0.2136 0.2345 REMARK 3 2 3.1622 - 2.5101 1.00 2968 151 0.2247 0.2773 REMARK 3 3 2.5101 - 2.1929 0.99 2940 136 0.2113 0.2250 REMARK 3 4 2.1929 - 1.9924 0.99 2884 166 0.2037 0.2659 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 1485 REMARK 3 ANGLE : 1.070 2019 REMARK 3 CHIRALITY : 0.047 252 REMARK 3 PLANARITY : 0.005 254 REMARK 3 DIHEDRAL : 12.390 521 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 5YM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005546. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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) : 0.97917 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 : 605729 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL 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 (%): 35.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA2HPO4:CITRIC ACID (PH 4.2), REMARK 280 22% (W/V) PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 41.93150 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 GLU A 57 REMARK 465 HIS A 73 REMARK 465 THR A 74 REMARK 465 VAL A 75 REMARK 465 GLY A 76 REMARK 465 GLY A 77 REMARK 465 LYS A 78 REMARK 465 GLN A 79 REMARK 465 THR A 106 REMARK 465 ILE A 107 REMARK 465 LEU A 108 REMARK 465 GLN A 109 REMARK 465 HIS A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 GLU B 57 REMARK 465 LEU B 108 REMARK 465 GLN B 109 REMARK 465 HIS B 110 REMARK 465 HIS B 111 REMARK 465 HIS B 112 REMARK 465 HIS B 113 REMARK 465 HIS B 114 REMARK 465 HIS B 115 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 THR A 34 OG1 CG2 REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 THR A 56 OG1 CG2 REMARK 470 THR A 105 OG1 CG2 REMARK 470 ARG B 33 CG CD NE CZ NH1 NH2 REMARK 470 THR B 34 OG1 CG2 REMARK 470 LYS B 36 CG CD CE NZ REMARK 470 THR B 56 OG1 CG2 REMARK 470 THR B 105 OG1 CG2 REMARK 470 THR B 106 OG1 CG2 REMARK 470 ILE B 107 CG1 CG2 CD1 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 ALA A 12 -150.52 -148.57 REMARK 500 ASN A 89 -6.73 70.78 REMARK 500 ASN A 89 -7.42 70.78 REMARK 500 ALA B 12 -149.57 -148.63 REMARK 500 THR B 105 -129.41 -91.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YM8 A 8 109 UNP X2G6C4 X2G6C4_9NIDO 3385 3486 DBREF 5YM8 B 8 109 UNP X2G6C4 X2G6C4_9NIDO 3385 3486 SEQADV 5YM8 HIS A 110 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS A 111 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS A 112 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS A 113 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS A 114 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS A 115 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS B 110 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS B 111 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS B 112 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS B 113 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS B 114 UNP X2G6C4 EXPRESSION TAG SEQADV 5YM8 HIS B 115 UNP X2G6C4 EXPRESSION TAG SEQRES 1 A 108 ASN VAL PHE THR ALA GLN ASN THR ALA GLN ASP PHE ASN SEQRES 2 A 108 GLY ASN GLU SER THR VAL LYS SER PHE TYR VAL THR ARG SEQRES 3 A 108 THR GLY LYS LYS ILE LEU VAL ALA ILE THR SER THR LYS SEQRES 4 A 108 ASP ASN LEU LYS THR VAL THR CYS LEU THR GLU THR GLY SEQRES 5 A 108 LYS THR VAL LEU ASN LEU ASP PRO PRO MET ARG PHE ALA SEQRES 6 A 108 HIS THR VAL GLY GLY LYS GLN SER VAL VAL TYR LEU TYR SEQRES 7 A 108 PHE ILE GLN ASN ILE SER SER LEU ASN ARG GLY MET VAL SEQRES 8 A 108 ILE GLY HIS ILE SER GLU THR THR ILE LEU GLN HIS HIS SEQRES 9 A 108 HIS HIS HIS HIS SEQRES 1 B 108 ASN VAL PHE THR ALA GLN ASN THR ALA GLN ASP PHE ASN SEQRES 2 B 108 GLY ASN GLU SER THR VAL LYS SER PHE TYR VAL THR ARG SEQRES 3 B 108 THR GLY LYS LYS ILE LEU VAL ALA ILE THR SER THR LYS SEQRES 4 B 108 ASP ASN LEU LYS THR VAL THR CYS LEU THR GLU THR GLY SEQRES 5 B 108 LYS THR VAL LEU ASN LEU ASP PRO PRO MET ARG PHE ALA SEQRES 6 B 108 HIS THR VAL GLY GLY LYS GLN SER VAL VAL TYR LEU TYR SEQRES 7 B 108 PHE ILE GLN ASN ILE SER SER LEU ASN ARG GLY MET VAL SEQRES 8 B 108 ILE GLY HIS ILE SER GLU THR THR ILE LEU GLN HIS HIS SEQRES 9 B 108 HIS HIS HIS HIS FORMUL 3 HOH *70(H2 O) HELIX 1 AA1 SER A 91 SER A 103 1 13 HELIX 2 AA2 SER B 91 SER B 103 1 13 SHEET 1 AA1 7 LYS A 60 ASN A 64 0 SHEET 2 AA1 7 LEU A 49 LEU A 55 -1 N CYS A 54 O THR A 61 SHEET 3 AA1 7 VAL A 9 ASP A 18 -1 N GLN A 17 O LYS A 50 SHEET 4 AA1 7 GLU A 23 ARG A 33 -1 O VAL A 26 N ASN A 14 SHEET 5 AA1 7 LYS A 36 SER A 44 -1 O VAL A 40 N PHE A 29 SHEET 6 AA1 7 VAL A 82 PHE A 86 -1 O TYR A 83 N SER A 44 SHEET 7 AA1 7 MET A 69 PHE A 71 -1 N MET A 69 O LEU A 84 SHEET 1 AA2 7 LYS B 60 ASN B 64 0 SHEET 2 AA2 7 LEU B 49 LEU B 55 -1 N CYS B 54 O THR B 61 SHEET 3 AA2 7 VAL B 9 ASP B 18 -1 N GLN B 17 O LYS B 50 SHEET 4 AA2 7 GLU B 23 ARG B 33 -1 O SER B 28 N ALA B 12 SHEET 5 AA2 7 LYS B 36 SER B 44 -1 O VAL B 40 N PHE B 29 SHEET 6 AA2 7 LYS B 78 PHE B 86 -1 O TYR B 83 N SER B 44 SHEET 7 AA2 7 MET B 69 VAL B 75 -1 N PHE B 71 O VAL B 82 CRYST1 31.546 83.863 36.344 90.00 106.08 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 0.031700 0.000000 0.009140 0.00000 SCALE2 0.000000 0.011924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028636 0.00000