HEADER VIRAL PROTEIN 26-JUL-23 8K75 TITLE N-TERMINAL DOMAIN OF FIPV NUCLEOCAPSID PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN,NC,PROTEIN N; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FELINE CORONAVIRUS (STRAIN FIPV WSU-79/1146); SOURCE 3 ORGANISM_COMMON: FCOV; SOURCE 4 ORGANISM_TAXID: 33734; SOURCE 5 GENE: N, 6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FIPV, NUCLEOCAPSID PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.T.ZHANG,R.LIANG,Y.J.SHI,G.Q.PENG REVDAT 1 31-JUL-24 8K75 0 JRNL AUTH J.T.ZHANG,R.LIANG,Y.J.SHI,G.Q.PENG JRNL TITL N-TERMINAL DOMAIN OF FIPV NUCLEOCAPSID PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 39396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2723 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1023 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.037 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.038 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.490 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1053 ; 0.016 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1007 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1421 ; 1.820 ; 1.656 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2315 ; 1.429 ; 1.592 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 123 ; 7.194 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 63 ;28.144 ;21.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 183 ;12.571 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;16.281 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 126 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1192 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 274 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 495 ; 1.415 ; 1.460 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 494 ; 1.369 ; 1.456 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 617 ; 2.090 ; 2.192 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 618 ; 2.088 ; 2.197 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 558 ; 2.484 ; 1.734 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 556 ; 2.431 ; 1.725 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 804 ; 3.590 ; 2.488 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1206 ; 5.235 ;18.465 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1150 ; 4.757 ;17.203 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8K75 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 01-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-23 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97861 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41565 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.18700 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE, 30% W/V REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000, VAPOR DIFFUSION, REMARK 280 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 30.45000 REMARK 290 SMTRY3 2 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 MET A 0 REMARK 465 SER A 1 REMARK 465 ARG A 2 REMARK 465 GLY A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ASN A 6 REMARK 465 ASN A 7 REMARK 465 ASP A 8 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 REMARK 465 HIS A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 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 LEU A 129 78.67 -107.03 REMARK 500 REMARK 500 REMARK: NULL DBREF 8K75 A 5 130 UNP P25909 NCAP_FIPV 27 152 SEQADV 8K75 MET A 0 UNP P25909 INITIATING METHIONINE SEQADV 8K75 SER A 1 UNP P25909 EXPRESSION TAG SEQADV 8K75 ARG A 2 UNP P25909 EXPRESSION TAG SEQADV 8K75 GLY A 3 UNP P25909 EXPRESSION TAG SEQADV 8K75 ARG A 4 UNP P25909 EXPRESSION TAG SEQADV 8K75 ILE A 103 UNP P25909 THR 125 CONFLICT SEQADV 8K75 LEU A 131 UNP P25909 EXPRESSION TAG SEQADV 8K75 GLU A 132 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 133 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 134 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 135 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 136 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 137 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 138 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 139 UNP P25909 EXPRESSION TAG SEQADV 8K75 HIS A 140 UNP P25909 EXPRESSION TAG SEQRES 1 A 141 MET SER ARG GLY ARG LYS ASN ASN ASP ILE PRO LEU SER SEQRES 2 A 141 PHE TYR ASN PRO ILE THR LEU GLU GLN GLY SER LYS PHE SEQRES 3 A 141 TRP ASN LEU CYS PRO ARG ASP LEU VAL PRO LYS GLY ILE SEQRES 4 A 141 GLY ASN LYS ASP GLN GLN ILE GLY TYR TRP ASN ARG GLN SEQRES 5 A 141 ILE ARG TYR ARG ILE VAL LYS GLY GLN ARG LYS GLU LEU SEQRES 6 A 141 ALA GLU ARG TRP PHE PHE TYR PHE LEU GLY THR GLY PRO SEQRES 7 A 141 HIS ALA ASP ALA LYS PHE LYS ASP LYS ILE ASP GLY VAL SEQRES 8 A 141 PHE TRP VAL ALA ARG ASP GLY ALA MET ASN LYS PRO ILE SEQRES 9 A 141 THR LEU GLY THR ARG GLY THR ASN ASN GLU SER LYS PRO SEQRES 10 A 141 LEU ARG PHE ASP GLY LYS ILE PRO PRO GLN PHE GLN LEU SEQRES 11 A 141 GLU LEU GLU HIS HIS HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *190(H2 O) HELIX 1 AA1 LYS A 24 CYS A 29 1 6 HELIX 2 AA2 ASN A 40 GLN A 43 5 4 SHEET 1 AA1 5 VAL A 90 ALA A 94 0 SHEET 2 AA1 5 ILE A 45 ARG A 50 -1 N GLY A 46 O VAL A 93 SHEET 3 AA1 5 ARG A 67 PHE A 72 -1 O TYR A 71 N TYR A 47 SHEET 4 AA1 5 ILE A 17 LEU A 19 -1 N ILE A 17 O TRP A 68 SHEET 5 AA1 5 PHE A 127 GLN A 128 -1 O GLN A 128 N THR A 18 SHEET 1 AA2 2 TYR A 54 VAL A 57 0 SHEET 2 AA2 2 GLN A 60 GLU A 63 -1 O GLN A 60 N VAL A 57 CRYST1 28.768 60.900 35.621 90.00 97.92 90.00 P 1 21 1 2 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 0.034761 0.000000 0.004836 0.00000 SCALE2 0.000000 0.016420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028344 0.00000