HEADER PROTEIN BINDING 10-JUL-18 6A8W TITLE CRYSTAL STRUCTURE OF THE FHA DOMAIN OF FAR9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 64; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 160-295; COMPND 5 SYNONYM: FACTOR ARREST PROTEIN 9; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: VPS64, FAR9, YDR200C, YD9346.10C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VARIANT: CODONPLUS KEYWDS FHA DOMAIN, PHOSPHOPEPTIDE RECOGNITION, HOMOLOG OF SLMAP, PROTEIN KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.CHEN,W.Q.ZHANG,Z.C.ZHOU REVDAT 1 10-JUL-19 6A8W 0 JRNL AUTH M.CHEN,Z.C.ZHOU JRNL TITL TOPOLOGICAL STRUCTURE AND DYNAMIC ASSEMBLY OF THE STRIPAK JRNL TITL 2 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2045 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 29.7108 - 4.5434 1.00 1237 133 0.2030 0.2259 REMARK 3 2 4.5434 - 3.6083 1.00 1251 132 0.1573 0.1787 REMARK 3 3 3.6083 - 3.1527 1.00 1239 135 0.1665 0.2189 REMARK 3 4 3.1527 - 2.8647 1.00 1244 142 0.1856 0.2052 REMARK 3 5 2.8647 - 2.6595 1.00 1215 139 0.1859 0.2280 REMARK 3 6 2.6595 - 2.5028 1.00 1247 139 0.1988 0.2630 REMARK 3 7 2.5028 - 2.3775 1.00 1247 141 0.1849 0.2520 REMARK 3 8 2.3775 - 2.2741 1.00 1205 135 0.1812 0.1835 REMARK 3 9 2.2741 - 2.1866 1.00 1260 136 0.1930 0.2320 REMARK 3 10 2.1866 - 2.1111 1.00 1224 135 0.1928 0.2811 REMARK 3 11 2.1111 - 2.0451 1.00 1240 138 0.1955 0.2245 REMARK 3 12 2.0451 - 1.9867 1.00 1216 135 0.2090 0.1960 REMARK 3 13 1.9867 - 1.9344 1.00 1275 135 0.2399 0.2911 REMARK 3 14 1.9344 - 1.8872 1.00 1215 141 0.2728 0.2807 REMARK 3 15 1.8872 - 1.8443 0.92 1143 129 0.2739 0.2684 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1001 REMARK 3 ANGLE : 0.875 1349 REMARK 3 CHIRALITY : 0.063 156 REMARK 3 PLANARITY : 0.004 176 REMARK 3 DIHEDRAL : 3.013 613 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: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I_MINUS AND I_PLUS COLUMNS. REMARK 4 REMARK 4 6A8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11148 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.18600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 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) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6%(V/V) TACSIMATE PH 6.0; 0.1M MES PH REMARK 280 6.0; 25%(W/V) POLYETHYLENE GLYCOL 4,000., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 15.99550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.70700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.99550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.70700 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 TOTAL BURIED SURFACE AREA: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 355 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 400 LIES ON A SPECIAL POSITION. 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 156 REMARK 465 ALA A 157 REMARK 465 VAL A 191 REMARK 465 THR A 192 REMARK 465 ASN A 193 REMARK 465 SER A 194 REMARK 465 VAL A 195 REMARK 465 ASN A 196 REMARK 465 LYS A 197 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 GLU A 172 CG CD OE1 OE2 REMARK 470 LYS A 186 CG CD CE NZ REMARK 470 ASN A 198 CG OD1 ND2 REMARK 470 LYS A 203 CG CD CE NZ REMARK 470 ARG A 204 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 206 CG CD1 CD2 REMARK 470 PHE A 207 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 209 CG CD OE1 NE2 REMARK 470 ARG A 225 CZ NH1 NH2 REMARK 470 ILE A 295 CG1 CG2 CD1 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 318 O HOH A 388 1.89 REMARK 500 O HOH A 399 O HOH A 414 1.97 REMARK 500 O HOH A 338 O HOH A 398 2.06 REMARK 500 O ASP A 275 O HOH A 301 2.13 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 LEU A 244 43.64 -104.79 REMARK 500 ARG A 258 -143.28 -123.41 REMARK 500 ASP A 275 132.89 66.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 6A8W A 160 295 UNP Q03944 VPS64_YEAST 160 295 SEQADV 6A8W GLY A 156 UNP Q03944 EXPRESSION TAG SEQADV 6A8W ALA A 157 UNP Q03944 EXPRESSION TAG SEQADV 6A8W MSE A 158 UNP Q03944 EXPRESSION TAG SEQADV 6A8W ALA A 159 UNP Q03944 EXPRESSION TAG SEQADV 6A8W MSE A 167 UNP Q03944 LEU 167 ENGINEERED MUTATION SEQADV 6A8W MSE A 269 UNP Q03944 THR 269 ENGINEERED MUTATION SEQRES 1 A 140 GLY ALA MSE ALA HIS ILE ILE ILE LEU LYS SER MSE ASN SEQRES 2 A 140 ALA THR PHE GLU THR LYS PHE LEU VAL VAL PRO PHE LYS SEQRES 3 A 140 PRO ASP GLY LEU LYS LEU GLY ARG PRO VAL THR ASN SER SEQRES 4 A 140 VAL ASN LYS ASN ASN SER GLY SER LYS ARG ASP LEU PHE SEQRES 5 A 140 SER GLN GLN VAL ARG PRO ASP ASN GLY ASN PHE ASP SER SEQRES 6 A 140 ARG VAL LEU SER ARG ASN HIS ALA CYS LEU SER CYS ASP SEQRES 7 A 140 PRO THR SER GLY LYS ILE TYR ILE ARG ASP LEU LYS SER SEQRES 8 A 140 SER ASN GLY THR PHE VAL ASN GLY VAL LYS ILE ARG GLN SEQRES 9 A 140 ASN ASP VAL GLU LEU LYS VAL GLY ASP MSE VAL ASP LEU SEQRES 10 A 140 GLY THR ASP ILE ASP SER LYS PHE GLU HIS ARG LYS ILE SEQRES 11 A 140 SER ALA TYR VAL GLU GLU ILE SER VAL ILE HET MSE A 158 8 HET MSE A 167 8 HET MSE A 269 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *118(H2 O) HELIX 1 AA1 GLY A 201 GLN A 209 1 9 SHEET 1 AA1 6 LYS A 174 VAL A 177 0 SHEET 2 AA1 6 HIS A 160 SER A 166 -1 N ILE A 162 O LEU A 176 SHEET 3 AA1 6 ILE A 285 VAL A 294 -1 O SER A 293 N ILE A 161 SHEET 4 AA1 6 MSE A 269 LEU A 272 -1 N VAL A 270 O ALA A 287 SHEET 5 AA1 6 THR A 250 VAL A 252 -1 N PHE A 251 O ASP A 271 SHEET 6 AA1 6 VAL A 255 LYS A 256 -1 O VAL A 255 N VAL A 252 SHEET 1 AA2 4 LEU A 185 LEU A 187 0 SHEET 2 AA2 4 ALA A 228 CYS A 232 -1 O LEU A 230 N LEU A 185 SHEET 3 AA2 4 ILE A 239 ASP A 243 -1 O TYR A 240 N SER A 231 SHEET 4 AA2 4 VAL A 262 LEU A 264 -1 O LEU A 264 N ILE A 239 LINK C MSE A 158 N ALA A 159 1555 1555 1.33 LINK C SER A 166 N MSE A 167 1555 1555 1.33 LINK C MSE A 167 N ASN A 168 1555 1555 1.33 LINK C ASP A 268 N MSE A 269 1555 1555 1.33 LINK C MSE A 269 N VAL A 270 1555 1555 1.32 CISPEP 1 LYS A 181 PRO A 182 0 8.91 CRYST1 31.991 59.414 64.984 90.00 90.00 90.00 P 21 21 2 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 0.031259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015388 0.00000 HETATM 1 N MSE A 158 23.527 28.564 3.316 1.00 41.78 N HETATM 2 CA MSE A 158 23.992 28.967 4.642 1.00 39.89 C HETATM 3 C MSE A 158 24.630 27.796 5.390 1.00 38.71 C HETATM 4 O MSE A 158 24.209 26.644 5.249 1.00 34.47 O HETATM 5 CB MSE A 158 22.839 29.542 5.467 1.00 44.55 C HETATM 6 CG MSE A 158 22.100 30.694 4.809 1.00 58.00 C HETATM 7 SE MSE A 158 23.113 32.362 4.764 1.00 97.61 SE HETATM 8 CE MSE A 158 23.302 32.652 6.678 1.00 51.06 C