HEADER VIRAL PROTEIN 16-DEC-05 2CA1 TITLE CRYSTAL STRUCTURE OF THE IBV CORONAVIRUS NUCLEOCAPSID COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN, RESIDUES 218-326; COMPND 5 SYNONYM: INFECTIOUS BRONCHITIS VIRUS NUCLEOCAPSID PROTEIN; COMPND 6 ENGINEERED: 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, VIRAL NUCLEOPROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.JAYARAM,H.FAN,B.R.BOWMAN,A.OOI,J.JAYARAM,E.W.COLLISON,J.LESCAR, AUTHOR 2 B.V.V.PRASAD REVDAT 4 08-MAY-24 2CA1 1 REMARK REVDAT 3 24-FEB-09 2CA1 1 VERSN REVDAT 2 10-APR-07 2CA1 1 REMARK REVDAT 1 19-JUN-06 2CA1 0 JRNL AUTH H.JAYARAM,H.FAN,B.R.BOWMAN,A.OOI,J.JAYARAM,E.W.COLLISON, JRNL AUTH 2 J.LESCAR,B.V.V.PRASAD JRNL TITL X-RAY STRUCTURES OF THE N- AND C-TERMINAL DOMAINS OF A JRNL TITL 2 CORONAVIRUS NUCLEOCAPSID PROTEIN: IMPLICATIONS FOR JRNL TITL 3 NUCLEOCAPSID FORMATION. JRNL REF J.VIROL. V. 80 6612 2006 JRNL REFN ISSN 0022-538X JRNL PMID 16775348 JRNL DOI 10.1128/JVI.00157-06 REMARK 2 REMARK 2 RESOLUTION. 2.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 9388 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) : 0.203 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 447 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.020 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 : 1680 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 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) : -0.81400 REMARK 3 B22 (A**2) : -0.81400 REMARK 3 B33 (A**2) : 1.62900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.352 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 : NULL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 37.58 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CA1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1290026869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31078 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 2.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 1.650 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.66 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.94000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.91000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.97000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 216 REMARK 465 MET B 217 REMARK 465 LYS B 218 REMARK 465 ALA B 219 REMARK 465 ASP B 220 REMARK 465 GLU B 221 REMARK 465 MET B 222 REMARK 465 ALA B 223 REMARK 465 HIS B 224 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 LYS A 249 CG CD CE NZ REMARK 470 GLY A 326 CA C O REMARK 470 LYS B 249 CG CD CE NZ 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 235 68.75 67.76 REMARK 500 VAL A 241 -45.87 -138.04 REMARK 500 THR A 246 -159.34 -111.03 REMARK 500 ASP A 325 -69.57 -126.06 REMARK 500 LYS B 247 -63.43 -93.67 REMARK 500 LYS B 290 117.19 -164.30 REMARK 500 PHE B 313 -68.89 -20.19 REMARK 500 ASP B 325 -87.82 -116.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 HIS-216 AND MET-217 COME FROM CLONING DBREF 2CA1 A 216 217 PDB 2CA1 2CA1 216 217 DBREF 2CA1 A 218 326 UNP Q4ZJS4 Q4ZJS4_9CORO 218 326 DBREF 2CA1 B 216 217 PDB 2CA1 2CA1 216 217 DBREF 2CA1 B 218 326 UNP Q4ZJS4 Q4ZJS4_9CORO 218 326 SEQRES 1 A 111 HIS MET LYS ALA ASP GLU MET ALA HIS ARG ARG TYR CYS SEQRES 2 A 111 LYS ARG THR ILE PRO PRO ASN TYR ARG VAL ASP GLN VAL SEQRES 3 A 111 PHE GLY PRO ARG THR LYS GLY LYS GLU GLY ASN PHE GLY SEQRES 4 A 111 ASP ASP LYS MET ASN GLU GLU GLY ILE LYS ASP GLY ARG SEQRES 5 A 111 VAL THR ALA MET LEU ASN LEU VAL PRO SER SER HIS ALA SEQRES 6 A 111 CYS LEU PHE GLY SER ARG VAL THR PRO LYS LEU GLN LEU SEQRES 7 A 111 ASP GLY LEU HIS LEU ARG PHE GLU PHE THR THR VAL VAL SEQRES 8 A 111 PRO CYS ASP ASP PRO GLN PHE ASP ASN TYR VAL LYS ILE SEQRES 9 A 111 CYS ASP GLN CYS VAL ASP GLY SEQRES 1 B 111 HIS MET LYS ALA ASP GLU MET ALA HIS ARG ARG TYR CYS SEQRES 2 B 111 LYS ARG THR ILE PRO PRO ASN TYR ARG VAL ASP GLN VAL SEQRES 3 B 111 PHE GLY PRO ARG THR LYS GLY LYS GLU GLY ASN PHE GLY SEQRES 4 B 111 ASP ASP LYS MET ASN GLU GLU GLY ILE LYS ASP GLY ARG SEQRES 5 B 111 VAL THR ALA MET LEU ASN LEU VAL PRO SER SER HIS ALA SEQRES 6 B 111 CYS LEU PHE GLY SER ARG VAL THR PRO LYS LEU GLN LEU SEQRES 7 B 111 ASP GLY LEU HIS LEU ARG PHE GLU PHE THR THR VAL VAL SEQRES 8 B 111 PRO CYS ASP ASP PRO GLN PHE ASP ASN TYR VAL LYS ILE SEQRES 9 B 111 CYS ASP GLN CYS VAL ASP GLY FORMUL 3 HOH *45(H2 O) HELIX 1 1 LYS A 218 HIS A 224 1 7 HELIX 2 2 ARG A 226 ARG A 230 5 5 HELIX 3 3 VAL A 238 GLY A 243 1 6 HELIX 4 4 ASP A 255 GLY A 262 1 8 HELIX 5 5 ASP A 265 ASN A 273 1 9 HELIX 6 6 SER A 277 SER A 285 1 9 HELIX 7 7 GLN A 312 VAL A 324 1 13 HELIX 8 8 ARG B 226 ARG B 230 5 5 HELIX 9 9 ARG B 237 VAL B 241 5 5 HELIX 10 10 ASP B 255 GLY B 262 1 8 HELIX 11 11 ASP B 265 LEU B 272 1 8 HELIX 12 12 SER B 277 GLY B 284 1 8 HELIX 13 13 GLN B 312 VAL B 324 1 13 SHEET 1 AA 4 ARG A 286 GLN A 292 0 SHEET 2 AA 4 GLY A 295 VAL A 306 -1 O GLY A 295 N GLN A 292 SHEET 3 AA 4 GLY B 295 VAL B 306 -1 O LEU B 296 N VAL A 306 SHEET 4 AA 4 ARG B 286 GLN B 292 -1 O ARG B 286 N GLU B 301 CRYST1 61.590 61.590 91.880 90.00 90.00 90.00 P 43 8 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 0.016236 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016236 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010884 0.00000 MTRIX1 1 -0.641080 -0.767420 0.009360 -4.51079 1 MTRIX2 1 -0.767110 0.640340 -0.038850 -1.64764 1 MTRIX3 1 0.023820 -0.032080 -0.999200 19.22127 1