HEADER VIRAL PROTEIN 06-MAY-20 7C20 TITLE CRYSTAL STRUCTURE OF RABIES VIRUS (NISHIGAHARA STRAIN) PHOSPHOPROTEIN TITLE 2 C-TERMINAL DOMAIN (K214A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN P,PROTEIN M1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RABIES VIRUS (STRAIN NISHIGAHARA RCEH); SOURCE 3 ORGANISM_COMMON: RABV; SOURCE 4 ORGANISM_TAXID: 11298; SOURCE 5 STRAIN: NISHIGAHARA RCEH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOPROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.NOMAI,K.MAENAKA,T.OSE REVDAT 2 29-NOV-23 7C20 1 REMARK REVDAT 1 17-MAR-21 7C20 0 JRNL AUTH A.SUGIYAMA,T.NOMAI,X.JIANG,M.MINAMI,M.YAO,K.MAENAKA,N.ITO, JRNL AUTH 2 P.R.GOOLEY,G.W.MOSELEY,T.OSE JRNL TITL STRUCTURAL COMPARISON OF THE C-TERMINAL DOMAIN OF JRNL TITL 2 FUNCTIONALLY DIVERGENT LYSSAVIRUS P PROTEINS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 529 507 2020 JRNL REFN ESSN 1090-2104 JRNL PMID 32703459 JRNL DOI 10.1016/J.BBRC.2020.05.195 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 2683 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.470 REMARK 3 FREE R VALUE TEST SET COUNT : 120 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 3.1070 - 3.0000 1.00 254 11 0.3362 0.3463 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.309 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.732 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.43 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 : 0.003 820 REMARK 3 ANGLE : 0.545 1105 REMARK 3 CHIRALITY : 0.033 124 REMARK 3 PLANARITY : 0.003 142 REMARK 3 DIHEDRAL : 2.249 502 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 7C20 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300016846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-15 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2984 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1VYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM HEPES-NAOH (PH 7.4), 150 MM REMARK 280 NACL, 3MM EDTA, 0.05% TWEEN20, SMALL TUBES, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 45.05400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.63250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.63250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.52700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.63250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.63250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.58100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.63250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.63250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.52700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.63250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.63250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.58100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.05400 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 GLY A 183 REMARK 465 HIS A 184 REMARK 465 MET A 185 REMARK 465 TRP A 186 REMARK 465 SER A 187 REMARK 465 ALA A 188 REMARK 465 THR A 189 REMARK 465 ASN A 190 REMARK 465 GLU A 191 REMARK 465 GLU A 192 REMARK 465 ASP A 193 REMARK 465 SER A 296 REMARK 465 CYS A 297 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 231 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 SER A 220 175.74 173.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 7C20 A 186 297 UNP Q9IPJ8 PHOSP_RABVN 186 297 SEQADV 7C20 GLY A 183 UNP Q9IPJ8 EXPRESSION TAG SEQADV 7C20 HIS A 184 UNP Q9IPJ8 EXPRESSION TAG SEQADV 7C20 MET A 185 UNP Q9IPJ8 EXPRESSION TAG SEQADV 7C20 ALA A 214 UNP Q9IPJ8 LYS 214 ENGINEERED MUTATION SEQRES 1 A 115 GLY HIS MET TRP SER ALA THR ASN GLU GLU ASP ASP LEU SEQRES 2 A 115 SER VAL GLU ALA GLU ILE ALA HIS GLN ILE ALA GLU SER SEQRES 3 A 115 PHE SER LYS LYS TYR ALA PHE PRO SER ARG SER SER GLY SEQRES 4 A 115 ILE PHE LEU TYR ASN PHE GLU GLN LEU LYS MET ASN LEU SEQRES 5 A 115 ASP ASP ILE VAL LYS GLU ALA LYS ASN VAL PRO GLY VAL SEQRES 6 A 115 THR ARG LEU ALA HIS ASP GLY SER LYS LEU PRO LEU ARG SEQRES 7 A 115 CYS VAL LEU GLY TRP VAL ALA LEU ALA ASN SER LYS LYS SEQRES 8 A 115 PHE GLN LEU LEU VAL GLU ALA ASN LYS LEU ASN LYS ILE SEQRES 9 A 115 MET GLN ASP ASP LEU ASN ARG TYR ALA SER CYS HELIX 1 AA1 LEU A 195 SER A 208 1 14 HELIX 2 AA2 ASN A 226 LYS A 231 5 6 HELIX 3 AA3 ASN A 233 LYS A 242 1 10 HELIX 4 AA4 GLY A 246 GLY A 254 1 9 HELIX 5 AA5 PRO A 258 SER A 271 1 14 HELIX 6 AA6 SER A 271 VAL A 278 1 8 HELIX 7 AA7 GLU A 279 TYR A 294 1 16 SHEET 1 AA1 2 TYR A 213 PRO A 216 0 SHEET 2 AA1 2 ILE A 222 TYR A 225 -1 O TYR A 225 N TYR A 213 CRYST1 51.265 51.265 90.108 90.00 90.00 90.00 P 41 21 2 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 0.019506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019506 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011098 0.00000