HEADER NUCLEOCAPSID PROTEIN 28-JUL-05 2BXX TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF IBV CORONAVIRUS TITLE 2 NUCLEOCAPSID. NATIVE CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RNA BINDING DOMAIN RESIDUES 29-160; COMPND 5 SYNONYM: INFECTIOUS BRONCHITIS VIRUS NUCLEOCAPSID PROTEIN, N COMPND 6 STRUCTURAL PROTEIN, NC; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AVIAN INFECTIOUS BRONCHITIS VIRUS; SOURCE 3 ORGANISM_TAXID: 11120; SOURCE 4 STRAIN: BEAUDETTE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOCAPSID PROTEIN, PHOSPHORYLATION, RNA-BINDING, VIRAL KEYWDS 2 NUCLEOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.FAN,A.OOI,D.-X.LIU,J.LESCAR REVDAT 4 13-DEC-23 2BXX 1 REMARK REVDAT 3 28-JUN-17 2BXX 1 REMARK REVDAT 2 24-FEB-09 2BXX 1 VERSN REVDAT 1 14-DEC-05 2BXX 0 JRNL AUTH H.FAN,A.OOI,Y.W.TAN,S.WANG,S.FANG,D.-X.LIU,J.LESCAR JRNL TITL THE NUCLEOCAPSID PROTEIN OF CORONAVIRUS INFECTIOUS JRNL TITL 2 BRONCHITIS VIRUS: CRYSTAL STRUCTURE OF ITS N-TERMINAL DOMAIN JRNL TITL 3 AND MULTIMERIZATION PROPERTIES. JRNL REF STRUCTURE V. 13 1859 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 16338414 JRNL DOI 10.1016/J.STR.2005.08.021 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKEIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 18921 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 SET) : 0.230 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1026 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2130 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.91000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 2.18000 REMARK 3 B13 (A**2) : 1.45000 REMARK 3 B23 (A**2) : 1.22000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.050 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2BXX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1290025091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2BTL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: PQS 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 85 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 85 TO CYS 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 ASN A 59 105.94 -161.93 REMARK 500 ASN A 61 41.10 -91.53 REMARK 500 ASN B 32 -126.49 30.66 REMARK 500 ALA B 33 134.19 150.68 REMARK 500 ASN B 61 34.85 -97.34 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 A2016 DISTANCE = 7.22 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BTL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF IBV CORONAVIRUS REMARK 900 NUCLEOCAPSID REMARK 999 REMARK 999 SEQUENCE REMARK 999 ENGINEERED MUTATION AT POSITION 85 DBREF 2BXX A 27 28 PDB 2BXX 2BXX 27 28 DBREF 2BXX A 29 160 UNP P69597 NCAP_IBVB 29 160 DBREF 2BXX B 27 28 PDB 2BXX 2BXX 27 28 DBREF 2BXX B 29 160 UNP P69597 NCAP_IBVB 29 160 SEQADV 2BXX CYS A 85 UNP P69597 LYS 85 ENGINEERED MUTATION SEQADV 2BXX CYS B 85 UNP P69597 LYS 85 ENGINEERED MUTATION SEQRES 1 A 134 HIS MET SER SER GLY ASN ALA SER TRP PHE GLN ALA ILE SEQRES 2 A 134 LYS ALA LYS LYS LEU ASN THR PRO PRO PRO LYS PHE GLU SEQRES 3 A 134 GLY SER GLY VAL PRO ASP ASN GLU ASN ILE LYS PRO SER SEQRES 4 A 134 GLN GLN HIS GLY TYR TRP ARG ARG GLN ALA ARG PHE LYS SEQRES 5 A 134 PRO GLY LYS GLY GLY ARG CYS PRO VAL PRO ASP ALA TRP SEQRES 6 A 134 TYR PHE TYR TYR THR GLY THR GLY PRO ALA ALA ASP LEU SEQRES 7 A 134 ASN TRP GLY ASP THR GLN ASP GLY ILE VAL TRP VAL ALA SEQRES 8 A 134 ALA LYS GLY ALA ASP THR LYS SER ARG SER ASN GLN GLY SEQRES 9 A 134 THR ARG ASP PRO ASP LYS PHE ASP GLN TYR PRO LEU ARG SEQRES 10 A 134 PHE SER ASP GLY GLY PRO ASP GLY ASN PHE ARG TRP ASP SEQRES 11 A 134 PHE ILE PRO LEU SEQRES 1 B 134 HIS MET SER SER GLY ASN ALA SER TRP PHE GLN ALA ILE SEQRES 2 B 134 LYS ALA LYS LYS LEU ASN THR PRO PRO PRO LYS PHE GLU SEQRES 3 B 134 GLY SER GLY VAL PRO ASP ASN GLU ASN ILE LYS PRO SER SEQRES 4 B 134 GLN GLN HIS GLY TYR TRP ARG ARG GLN ALA ARG PHE LYS SEQRES 5 B 134 PRO GLY LYS GLY GLY ARG CYS PRO VAL PRO ASP ALA TRP SEQRES 6 B 134 TYR PHE TYR TYR THR GLY THR GLY PRO ALA ALA ASP LEU SEQRES 7 B 134 ASN TRP GLY ASP THR GLN ASP GLY ILE VAL TRP VAL ALA SEQRES 8 B 134 ALA LYS GLY ALA ASP THR LYS SER ARG SER ASN GLN GLY SEQRES 9 B 134 THR ARG ASP PRO ASP LYS PHE ASP GLN TYR PRO LEU ARG SEQRES 10 B 134 PHE SER ASP GLY GLY PRO ASP GLY ASN PHE ARG TRP ASP SEQRES 11 B 134 PHE ILE PRO LEU FORMUL 3 HOH *187(H2 O) HELIX 1 1 LYS A 63 GLN A 66 5 4 HELIX 2 2 LYS B 63 GLN B 66 5 4 SHEET 1 AA 5 ILE A 113 ALA A 117 0 SHEET 2 AA 5 HIS A 68 PRO A 79 -1 O GLY A 69 N VAL A 116 SHEET 3 AA 5 ARG A 84 TYR A 95 -1 O CYS A 85 N LYS A 78 SHEET 4 AA 5 ILE A 39 ALA A 41 -1 O ILE A 39 N TRP A 91 SHEET 5 AA 5 PHE A 153 ARG A 154 -1 O ARG A 154 N LYS A 40 SHEET 1 AB 2 PHE A 51 GLU A 52 0 SHEET 2 AB 2 GLY A 148 PRO A 149 -1 O GLY A 148 N GLU A 52 SHEET 1 BA 5 ILE B 113 ALA B 117 0 SHEET 2 BA 5 HIS B 68 GLY B 80 -1 O GLY B 69 N VAL B 116 SHEET 3 BA 5 GLY B 83 TYR B 95 -1 O GLY B 83 N GLY B 80 SHEET 4 BA 5 ILE B 39 ALA B 41 -1 O ILE B 39 N TRP B 91 SHEET 5 BA 5 PHE B 153 ARG B 154 -1 O ARG B 154 N LYS B 40 CRYST1 35.422 35.776 55.860 99.20 94.07 108.96 P 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 0.028231 0.009699 0.003965 0.00000 SCALE2 0.000000 0.029555 0.005842 0.00000 SCALE3 0.000000 0.000000 0.018294 0.00000 MTRIX1 1 0.376000 -0.927000 0.003000 1.56722 1 MTRIX2 1 -0.926000 -0.376000 -0.027000 -3.17674 1 MTRIX3 1 0.026000 0.007000 -1.000000 16.00610 1