HEADER HYDROLASE 16-MAR-17 5XBC TITLE CRYSTAL STRUCTURE BASIS FOR PEDV NSP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NSP1 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 2-110; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORCINE EPIDEMIC DIARRHEA VIRUS; SOURCE 3 ORGANISM_TAXID: 28295; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS PORCINE EPIDEMIC DIARRHEA VIRUS, NSP1, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.SHEN,G.Q.PENG REVDAT 2 27-MAR-24 5XBC 1 REMARK REVDAT 1 13-DEC-17 5XBC 0 JRNL AUTH Z.SHEN,G.Q.PENG JRNL TITL CRYSTAL STRUCTURE BASIS FOR PEDV NSP1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.25 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 52517 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2681 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 26.4832 - 3.3307 0.93 2522 141 0.1635 0.1865 REMARK 3 2 3.3307 - 2.6445 1.00 2618 162 0.1666 0.1906 REMARK 3 3 2.6445 - 2.3104 1.00 2645 137 0.1823 0.1935 REMARK 3 4 2.3104 - 2.0993 1.00 2669 135 0.1668 0.1680 REMARK 3 5 2.0993 - 1.9489 0.99 2636 129 0.1588 0.1685 REMARK 3 6 1.9489 - 1.8340 1.00 2623 141 0.1558 0.1857 REMARK 3 7 1.8340 - 1.7422 1.00 2611 176 0.1619 0.1779 REMARK 3 8 1.7422 - 1.6663 1.00 2662 138 0.1569 0.1922 REMARK 3 9 1.6663 - 1.6022 1.00 2614 135 0.1635 0.1982 REMARK 3 10 1.6022 - 1.5469 1.00 2645 127 0.1645 0.1740 REMARK 3 11 1.5469 - 1.4986 1.00 2633 125 0.1691 0.2355 REMARK 3 12 1.4986 - 1.4557 1.00 2678 113 0.1726 0.2357 REMARK 3 13 1.4557 - 1.4174 1.00 2645 129 0.1782 0.2189 REMARK 3 14 1.4174 - 1.3828 1.00 2649 106 0.1820 0.2169 REMARK 3 15 1.3828 - 1.3514 1.00 2632 155 0.1985 0.2488 REMARK 3 16 1.3514 - 1.3226 0.99 2612 168 0.2084 0.2273 REMARK 3 17 1.3226 - 1.2962 1.00 2571 151 0.2235 0.2465 REMARK 3 18 1.2962 - 1.2717 0.99 2615 172 0.2367 0.2551 REMARK 3 19 1.2717 - 1.2490 0.99 2556 141 0.2454 0.2568 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.090 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 : 0.006 1885 REMARK 3 ANGLE : 0.991 2557 REMARK 3 CHIRALITY : 0.041 275 REMARK 3 PLANARITY : 0.005 334 REMARK 3 DIHEDRAL : 14.161 633 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 5XBC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000, HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52517 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 37.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43600 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: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.5, 18% W/V POLYETHYLENE REMARK 280 GLYCOL 1,000, 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 37.52650 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 A 118 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 NE2 GLN B 4 OE1 GLU B 99 2.13 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 THR A 68 -95.13 -124.00 REMARK 500 THR B 68 -93.76 -123.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 374 DISTANCE = 6.17 ANGSTROMS DBREF1 5XBC A 1 109 UNP A0A1N7TG28_9ALPC DBREF2 5XBC A A0A1N7TG28 2 110 DBREF1 5XBC B 1 109 UNP A0A1N7TG28_9ALPC DBREF2 5XBC B A0A1N7TG28 2 110 SEQADV 5XBC LEU A 110 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC GLU A 111 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS A 112 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS A 113 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS A 114 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS A 115 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS A 116 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS A 117 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS A 118 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC LEU B 110 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC GLU B 111 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS B 112 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS B 113 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS B 114 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS B 115 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS B 116 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS B 117 UNP A0A1N7TG2 EXPRESSION TAG SEQADV 5XBC HIS B 118 UNP A0A1N7TG2 EXPRESSION TAG SEQRES 1 A 118 ALA SER ASN GLN VAL THR LEU ALA PHE ALA ASN ASP ALA SEQRES 2 A 118 GLU ILE SER ALA PHE GLY PHE CYS THR ALA SER GLU ALA SEQRES 3 A 118 VAL SER TYR TYR SER GLU ALA ALA ALA SER GLY PHE MET SEQRES 4 A 118 GLN CYS ARG PHE VAL SER PHE ASP LEU ALA ASP THR VAL SEQRES 5 A 118 GLU GLY LEU LEU PRO GLU ASP TYR VAL MET VAL VAL VAL SEQRES 6 A 118 GLY THR THR LYS LEU SER ALA TYR VAL ASP THR PHE GLY SEQRES 7 A 118 SER ARG PRO ARG ASN ILE CYS GLY TRP LEU LEU PHE SER SEQRES 8 A 118 ASN CYS ASN TYR PHE LEU GLU GLU LEU GLU LEU THR PHE SEQRES 9 A 118 GLY ARG ARG GLY GLY LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 10 A 118 HIS SEQRES 1 B 118 ALA SER ASN GLN VAL THR LEU ALA PHE ALA ASN ASP ALA SEQRES 2 B 118 GLU ILE SER ALA PHE GLY PHE CYS THR ALA SER GLU ALA SEQRES 3 B 118 VAL SER TYR TYR SER GLU ALA ALA ALA SER GLY PHE MET SEQRES 4 B 118 GLN CYS ARG PHE VAL SER PHE ASP LEU ALA ASP THR VAL SEQRES 5 B 118 GLU GLY LEU LEU PRO GLU ASP TYR VAL MET VAL VAL VAL SEQRES 6 B 118 GLY THR THR LYS LEU SER ALA TYR VAL ASP THR PHE GLY SEQRES 7 B 118 SER ARG PRO ARG ASN ILE CYS GLY TRP LEU LEU PHE SER SEQRES 8 B 118 ASN CYS ASN TYR PHE LEU GLU GLU LEU GLU LEU THR PHE SEQRES 9 B 118 GLY ARG ARG GLY GLY LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 10 B 118 HIS FORMUL 3 HOH *348(H2 O) HELIX 1 AA1 THR A 22 SER A 36 1 15 HELIX 2 AA2 ASP A 47 ASP A 50 5 4 HELIX 3 AA3 THR B 22 SER B 36 1 15 HELIX 4 AA4 ASP B 47 ASP B 50 5 4 SHEET 1 AA1 9 VAL A 52 GLU A 53 0 SHEET 2 AA1 9 ILE A 15 PHE A 18 1 N ALA A 17 O GLU A 53 SHEET 3 AA1 9 ILE A 84 SER A 91 -1 O PHE A 90 N PHE A 18 SHEET 4 AA1 9 TYR A 60 VAL A 65 -1 N VAL A 64 O CYS A 85 SHEET 5 AA1 9 LEU A 70 THR A 76 -1 O ASP A 75 N VAL A 61 SHEET 6 AA1 9 TYR A 95 PHE A 104 1 O THR A 103 N ALA A 72 SHEET 7 AA1 9 GLN A 4 ALA A 10 -1 N LEU A 7 O GLU A 98 SHEET 8 AA1 9 CYS A 41 SER A 45 1 O PHE A 43 N ALA A 10 SHEET 9 AA1 9 ILE A 84 SER A 91 -1 O TRP A 87 N VAL A 44 SHEET 1 AA2 9 VAL B 52 GLU B 53 0 SHEET 2 AA2 9 ILE B 15 PHE B 18 1 N ILE B 15 O GLU B 53 SHEET 3 AA2 9 ILE B 84 SER B 91 -1 O PHE B 90 N PHE B 18 SHEET 4 AA2 9 TYR B 60 VAL B 65 -1 N VAL B 64 O CYS B 85 SHEET 5 AA2 9 LEU B 70 THR B 76 -1 O ASP B 75 N VAL B 61 SHEET 6 AA2 9 TYR B 95 PHE B 104 1 O THR B 103 N ALA B 72 SHEET 7 AA2 9 GLN B 4 ALA B 10 -1 N LEU B 7 O GLU B 98 SHEET 8 AA2 9 CYS B 41 SER B 45 1 O PHE B 43 N ALA B 10 SHEET 9 AA2 9 ILE B 84 SER B 91 -1 O TRP B 87 N VAL B 44 CRYST1 34.709 75.053 37.363 90.00 89.96 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 0.028811 0.000000 -0.000019 0.00000 SCALE2 0.000000 0.013324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026764 0.00000