HEADER VIRAL PROTEIN 12-DEC-21 7T5H TITLE STRUCTURE OF RABIES VIRUS PHOSPHOPROTEIN C-TERMINAL DOMAIN, WILD TYPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: PROTEIN P,PROTEIN M1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RABIES VIRUS NISHIGAHARA RCEH; SOURCE 3 ORGANISM_TAXID: 11298; SOURCE 4 STRAIN: NISHIGAHARA RCEH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS RABIES, PHOSPHOPROTEIN, VIRUS, LYSSAVIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHAN,R.D.METCALFE,P.R.GOOLEY,M.D.W.GRIFFIN REVDAT 3 18-OCT-23 7T5H 1 REMARK REVDAT 2 25-MAY-22 7T5H 1 JRNL REVDAT 1 20-APR-22 7T5H 0 JRNL AUTH J.ZHAN,E.WATTS,A.M.BRICE,R.D.METCALFE,A.M.ROZARIO,A.SETHI, JRNL AUTH 2 F.YAN,T.D.M.BELL,M.D.W.GRIFFIN,G.W.MOSELEY,P.R.GOOLEY JRNL TITL MOLECULAR BASIS OF FUNCTIONAL EFFECTS OF PHOSPHORYLATION OF JRNL TITL 2 THE C-TERMINAL DOMAIN OF THE RABIES VIRUS P PROTEIN. JRNL REF J.VIROL. V. 96 11122 2022 JRNL REFN ESSN 1098-5514 JRNL PMID 35404083 JRNL DOI 10.1128/JVI.00111-22 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 949 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 34.8300 - 2.8700 1.00 2701 155 0.1685 0.2072 REMARK 3 2 2.8700 - 2.2800 1.00 2609 102 0.1818 0.1580 REMARK 3 3 2.2800 - 1.9900 1.00 2555 146 0.1833 0.2186 REMARK 3 4 1.9900 - 1.8100 1.00 2533 143 0.2134 0.2531 REMARK 3 5 1.8100 - 1.6800 1.00 2530 140 0.2146 0.2594 REMARK 3 6 1.6800 - 1.5800 1.00 2525 119 0.2743 0.2678 REMARK 3 7 1.5800 - 1.5000 1.00 2510 144 0.2518 0.2853 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) : 0.138 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.944 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.07 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 : 0.007 902 REMARK 3 ANGLE : 0.873 1214 REMARK 3 CHIRALITY : 0.040 131 REMARK 3 PLANARITY : 0.011 156 REMARK 3 DIHEDRAL : 12.199 341 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 190 THROUGH 297) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2057 -9.7654 11.4349 REMARK 3 T TENSOR REMARK 3 T11: 0.1575 T22: 0.1222 REMARK 3 T33: 0.1019 T12: 0.0220 REMARK 3 T13: -0.0028 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 4.0141 L22: 3.4321 REMARK 3 L33: 2.0371 L12: 1.7015 REMARK 3 L13: -0.2695 L23: -0.6808 REMARK 3 S TENSOR REMARK 3 S11: -0.1195 S12: 0.0036 S13: 0.0026 REMARK 3 S21: -0.0251 S22: 0.0875 S23: 0.0638 REMARK 3 S31: -0.1295 S32: -0.0859 S33: 0.0333 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 7T5H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000261043. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18982 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 43.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.46300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1VYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9 M AMMONIUM SULFATE, 0.2 M REMARK 280 POTASSIUM SODIUM TARTRATE AND 0.1 M SODIUM CITRATE (PH 4.75), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 21.15600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.66300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.99350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.66300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.15600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.99350 REMARK 290 SMTRY3 4 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 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 471 O HOH A 495 1.90 REMARK 500 O4 PO4 A 304 O HOH A 401 2.15 REMARK 500 O HOH A 453 O HOH A 458 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 219 -77.70 -73.50 REMARK 500 REMARK 500 REMARK: NULL DBREF 7T5H A 186 297 UNP Q9IPJ8 PHOSP_RABVN 186 297 SEQADV 7T5H GLY A 183 UNP Q9IPJ8 EXPRESSION TAG SEQADV 7T5H HIS A 184 UNP Q9IPJ8 EXPRESSION TAG SEQADV 7T5H MET A 185 UNP Q9IPJ8 EXPRESSION TAG SEQADV 7T5H SER A 297 UNP Q9IPJ8 CYS 297 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 LYS 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 SER HET EDO A 301 10 HET SO4 A 302 5 HET SO4 A 303 5 HET PO4 A 304 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM PO4 PHOSPHATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 PO4 O4 P 3- FORMUL 6 HOH *103(H2 O) HELIX 1 AA1 ASN A 190 SER A 208 1 19 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 ASP A 253 1 8 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 SER A 296 1 18 SHEET 1 AA1 2 TYR A 213 PRO A 216 0 SHEET 2 AA1 2 ILE A 222 TYR A 225 -1 O PHE A 223 N PHE A 215 CRYST1 42.312 43.987 61.326 90.00 90.00 90.00 P 21 21 21 4 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 0.023634 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016306 0.00000