HEADER RNA BINDING PROTEIN 11-JUL-13 4LMT
TITLE STRUCTURE OF THE N-TERMINAL DOMAIN OF CORONAVIRUS NUCLEOCAPSID PROTEIN
TITLE 2 COMPLEXED WITH NSC663284
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NUCLEOPROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 55-188;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN CORONAVIRUS;
SOURCE 3 ORGANISM_COMMON: HCOV-OC43;
SOURCE 4 ORGANISM_TAXID: 31631;
SOURCE 5 STRAIN: OC43;
SOURCE 6 GENE: N;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HCOV-OC43, NUCLEOCAPSID PRTOEIN, N-TERMAINL DOMAIN, RNA BINDING, RNA
KEYWDS 2 BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.Y.LIN,C.L.LIU,M.H.HOU
REVDAT 2 08-NOV-23 4LMT 1 REMARK SEQADV
REVDAT 1 16-JUL-14 4LMT 0
JRNL AUTH S.Y.LIN,C.L.LIU,M.H.HOU
JRNL TITL DOMAIN OF CORONAVIRUS NUCLEOCAPSID PROTEIN COMPLEXED WITH
JRNL TITL 2 NSC663284
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.71 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168)
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 : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.73
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2
REMARK 3 NUMBER OF REFLECTIONS : 17133
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.240
REMARK 3 R VALUE (WORKING SET) : 0.236
REMARK 3 FREE R VALUE : 0.279
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980
REMARK 3 FREE R VALUE TEST SET COUNT : 1710
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 22.7344 - 3.9081 0.53 1380 144 0.1853 0.2089
REMARK 3 2 3.9081 - 3.1045 0.46 1208 132 0.2037 0.2343
REMARK 3 3 3.1045 - 2.7128 0.52 1346 151 0.2305 0.2698
REMARK 3 4 2.7128 - 2.4651 0.51 1355 149 0.2560 0.3134
REMARK 3 5 2.4651 - 2.2886 0.51 1335 146 0.2528 0.3041
REMARK 3 6 2.2886 - 2.1537 0.42 1087 123 0.2797 0.3189
REMARK 3 7 2.1537 - 2.0460 0.51 1327 148 0.2506 0.3257
REMARK 3 8 2.0460 - 1.9569 0.51 1347 156 0.2592 0.3168
REMARK 3 9 1.9569 - 1.8816 0.51 1327 143 0.3119 0.3352
REMARK 3 10 1.8816 - 1.8167 0.51 1348 152 0.2676 0.3091
REMARK 3 11 1.8167 - 1.7600 0.49 1281 142 0.2575 0.2887
REMARK 3 12 1.7600 - 1.7097 0.42 1082 124 0.2552 0.3509
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) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.560
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 13.13
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.38
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 : 0.008 1143
REMARK 3 ANGLE : 1.373 1563
REMARK 3 CHIRALITY : 0.091 154
REMARK 3 PLANARITY : 0.006 205
REMARK 3 DIHEDRAL : 18.076 411
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 4LMT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-AUG-13.
REMARK 100 THE DEPOSITION ID IS D_1000080826.
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
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSRRC
REMARK 200 BEAMLINE : BL13B1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1
REMARK 200 MONOCHROMATOR : LN2-COOLED, FIXED-EXIT DOUBLE
REMARK 200 CRYSTAL MONOCHROMATOR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17432
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: 4J3K
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.26
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG1500, 0.25M SPG, PH 7.5, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.58200
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.29100
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.43650
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.14550
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.72750
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 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 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 GLN A 116
REMARK 465 ARG A 117
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 ARG A 107 140.48 59.48
REMARK 500 THR A 111 -160.39 -117.89
REMARK 500 ASP A 113 -108.50 -89.99
REMARK 500 ASP A 165 159.02 88.65
REMARK 500 PRO A 166 -120.39 -69.73
REMARK 500 SER A 167 24.47 -79.04
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CQD A 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4LM7 RELATED DB: PDB
REMARK 900 RELATED ID: 4LM9 RELATED DB: PDB
REMARK 900 RELATED ID: 4LMC RELATED DB: PDB
DBREF 4LMT A 58 191 UNP Q6SA23 Q6SA23_CVHOC 55 188
SEQADV 4LMT GLU A 56 UNP Q6SA23 EXPRESSION TAG
SEQADV 4LMT PHE A 57 UNP Q6SA23 EXPRESSION TAG
SEQRES 1 A 136 GLU PHE ASN VAL VAL PRO TYR TYR SER TRP PHE SER GLY
SEQRES 2 A 136 ILE THR GLN PHE GLN LYS GLY LYS GLU PHE GLU PHE VAL
SEQRES 3 A 136 GLU GLY GLN GLY VAL PRO ILE ALA PRO GLY VAL PRO ALA
SEQRES 4 A 136 THR GLU ALA LYS GLY TYR TRP TYR ARG HIS ASN ARG ARG
SEQRES 5 A 136 SER PHE LYS THR ALA ASP GLY ASN GLN ARG GLN LEU LEU
SEQRES 6 A 136 PRO ARG TRP TYR PHE TYR TYR LEU GLY THR GLY PRO HIS
SEQRES 7 A 136 ALA LYS ASP GLN TYR GLY THR ASP ILE ASP GLY VAL TYR
SEQRES 8 A 136 TRP VAL ALA SER ASN GLN ALA ASP VAL ASN THR PRO ALA
SEQRES 9 A 136 ASP ILE VAL ASP ARG ASP PRO SER SER ASP GLU ALA ILE
SEQRES 10 A 136 PRO THR ARG PHE PRO PRO GLY THR VAL LEU PRO GLN GLY
SEQRES 11 A 136 TYR TYR ILE GLU GLY SER
HET CQD A 201 22
HETNAM CQD 6-CHLORO-7-{[2-(MORPHOLIN-4-YL)ETHYL]AMINO}QUINOLINE-5,
HETNAM 2 CQD 8-DIONE
FORMUL 2 CQD C15 H16 CL N3 O3
FORMUL 3 HOH *99(H2 O)
HELIX 1 1 PRO A 93 GLU A 96 5 4
HELIX 2 2 THR A 130 ALA A 134 5 5
SHEET 1 A 5 VAL A 145 ALA A 149 0
SHEET 2 A 5 LYS A 98 HIS A 104 -1 N TRP A 101 O TYR A 146
SHEET 3 A 5 ARG A 122 TYR A 127 -1 O TYR A 126 N TYR A 100
SHEET 4 A 5 ILE A 69 GLN A 71 -1 N ILE A 69 O TRP A 123
SHEET 5 A 5 TYR A 186 ILE A 188 -1 O TYR A 187 N THR A 70
CISPEP 1 ASP A 165 PRO A 166 0 11.62
SITE 1 AC1 10 PHE A 57 PRO A 61 TYR A 62 TYR A 63
SITE 2 AC1 10 SER A 64 TYR A 124 TYR A 126 ARG A 164
SITE 3 AC1 10 GLU A 170 ALA A 171
CRYST1 81.911 81.911 42.873 90.00 90.00 120.00 P 65 6
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 0.012208 0.007049 0.000000 0.00000
SCALE2 0.000000 0.014097 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023325 0.00000