HEADER HYDROLASE 01-JUN-21 7EZN TITLE CRYSTAL STRUCTURE OF CNYVH1 COMPLEX WITH VANADATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-TYROSINE-PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.3.48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRYPTOCOCCUS NEOFORMANS VAR. GRUBII SEROTYPE A SOURCE 3 (STRAIN H99 / ATCC 208821 / CBS 10515 / FGSC 9487); SOURCE 4 ORGANISM_COMMON: FILOBASIDIELLA NEOFORMANS VAR. GRUBII; SOURCE 5 ORGANISM_TAXID: 235443; SOURCE 6 STRAIN: H99 / ATCC 208821 / CBS 10515 / FGSC 9487; SOURCE 7 GENE: CNAG_01203; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DUSP, PHOSPHATASE, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.K.CHOI,Y.YOO REVDAT 2 29-NOV-23 7EZN 1 REMARK REVDAT 1 08-JUN-22 7EZN 0 JRNL AUTH M.K.CHOI,Y.YOO JRNL TITL CRYSTAL STRUCTURE OF CNYVH1 COMPLEX WITH VANADATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.G.JEONG,C.H.WEI,B.KU,T.J.JEON,P.N.CHIEN,J.K.KIM,S.Y.PARK, REMARK 1 AUTH 2 H.S.HWANG,S.Y.RYU,H.PARK,D.S.KIM,S.J.KIM,S.E.RYU REMARK 1 TITL THE FAMILY-WIDE STRUCTURE AND FUNCTION OF HUMAN REMARK 1 TITL 2 DUAL-SPECIFICITY PROTEIN PHOSPHATASES. REMARK 1 REF ACTA CRYSTALLOGR D BIOL V. 70 421 2014 REMARK 1 REF 2 CRYSTALLOGR REMARK 1 REFN ESSN 1399-0047 REMARK 1 DOI 10.1107/S1399004713029866 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 24168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1800 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 33.1000 - 4.2300 0.98 1952 158 0.1741 0.1772 REMARK 3 2 4.2300 - 3.3600 1.00 1861 149 0.1738 0.1927 REMARK 3 3 3.3600 - 2.9300 1.00 1830 148 0.2204 0.2081 REMARK 3 4 2.9300 - 2.6700 1.00 1843 149 0.2136 0.2188 REMARK 3 5 2.6700 - 2.4800 1.00 1806 143 0.2304 0.2407 REMARK 3 6 2.4700 - 2.3300 1.00 1802 146 0.2122 0.2140 REMARK 3 7 2.3300 - 2.2100 1.00 1780 144 0.2177 0.2355 REMARK 3 8 2.2100 - 2.1200 1.00 1792 143 0.2174 0.2057 REMARK 3 9 2.1200 - 2.0300 0.99 1782 143 0.2110 0.2537 REMARK 3 10 2.0300 - 1.9600 0.99 1774 143 0.2308 0.2744 REMARK 3 11 1.9600 - 1.9000 0.89 1577 127 0.2283 0.2737 REMARK 3 12 1.9000 - 1.8500 0.77 1382 111 0.2337 0.2280 REMARK 3 13 1.8500 - 1.8000 0.67 1187 96 0.2532 0.2371 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) : 0.135 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.601 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.94 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 : 0.009 1404 REMARK 3 ANGLE : 1.545 1900 REMARK 3 CHIRALITY : 0.072 212 REMARK 3 PLANARITY : 0.006 244 REMARK 3 DIHEDRAL : 13.397 524 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 7EZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24183 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 33.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01125 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21280 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 4KI9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16 M MAGNESIUM CHLORIDE, 0.08 M TRIS REMARK 280 -HCL PH 8.5, 24 % (W/V) PEG 4000, 20 % GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 60.16200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.09700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.09700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.08100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.09700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.09700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.24300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.09700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.09700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.08100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.09700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.09700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 90.24300 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 60.16200 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: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 504 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 575 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 LYS A 110 REMARK 465 GLU A 111 REMARK 465 ALA A 112 REMARK 465 MET A 113 REMARK 465 GLU A 197 REMARK 465 PRO A 198 REMARK 465 SER A 199 REMARK 465 SER A 200 REMARK 465 GLN A 201 REMARK 465 LYS A 202 REMARK 465 ASN A 203 REMARK 465 GLY A 204 REMARK 465 THR A 205 REMARK 465 GLU A 206 REMARK 465 ASN A 207 REMARK 465 GLY A 208 REMARK 465 GLU A 209 REMARK 465 SER A 210 REMARK 465 LEU A 211 REMARK 465 LYS A 212 REMARK 465 THR A 305 REMARK 465 THR A 306 REMARK 465 THR A 307 REMARK 465 GLN A 308 REMARK 465 PHE A 309 REMARK 465 ILE A 310 REMARK 465 ASN A 311 REMARK 465 GLY A 312 REMARK 465 ASP A 313 REMARK 465 GLY A 314 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 ASP A 127 -169.64 -107.74 REMARK 500 ASP A 168 64.85 -105.02 REMARK 500 CYS A 233 -153.45 -135.62 REMARK 500 SER A 238 -75.12 -122.53 REMARK 500 GLU A 271 96.78 -166.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EZN A 110 314 UNP J9VTB5 J9VTB5_CRYNH 110 314 SEQRES 1 A 205 LYS GLU ALA MET GLY HIS MET GLN GLU VAL VAL ASP GLY SEQRES 2 A 205 LEU TRP VAL GLY ASP LEU VAL ALA ALA ASN ASP ASP ASP SEQRES 3 A 205 GLU LEU GLU LYS ASN GLY ILE LYS ASN ILE LEU SER ALA SEQRES 4 A 205 LEU ARG PRO SER LEU LYS PHE SER ASP LYS TYR ALA VAL SEQRES 5 A 205 TYR PRO LEU GLU ILE ASP ASP SER ALA ASP THR ASP LEU SEQRES 6 A 205 LEU SER HIS LEU PRO SER CYS VAL ALA TRP ILE LYS GLU SEQRES 7 A 205 ILE LEU ASP LEU ARG GLN LYS ALA ALA GLU PRO SER SER SEQRES 8 A 205 GLN LYS ASN GLY THR GLU ASN GLY GLU SER LEU LYS ARG SEQRES 9 A 205 SER PRO ASP ILE ASP THR VAL ALA GLN PRO GLY LYS PRO SEQRES 10 A 205 GLY GLY VAL LEU VAL HIS CYS GLN ALA GLY MET SER ARG SEQRES 11 A 205 SER ALA SER ILE VAL ALA ALA TYR LEU MET SER GLN TYR SEQRES 12 A 205 ASP LEU ASP PRO MET GLU ALA MET THR MET ILE ARG GLU SEQRES 13 A 205 LYS ARG PRO VAL VAL GLU PRO SER ALA THR PHE TRP HIS SEQRES 14 A 205 GLN LEU GLY LEU PHE TYR THR THR ASP GLY LYS VAL SER SEQRES 15 A 205 LEU LYS ASP ARG SER THR ARG GLN TYR TYR MET GLU ARG SEQRES 16 A 205 THR THR THR GLN PHE ILE ASN GLY ASP GLY HET VO4 A 401 5 HET EDO A 402 4 HETNAM VO4 VANADATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 VO4 O4 V 3- FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *76(H2 O) HELIX 1 AA1 ASP A 127 ASP A 133 1 7 HELIX 2 AA2 ASP A 133 ASN A 140 1 8 HELIX 3 AA3 LEU A 174 SER A 176 5 3 HELIX 4 AA4 HIS A 177 ALA A 196 1 20 HELIX 5 AA5 SER A 238 ASP A 253 1 16 HELIX 6 AA6 ASP A 255 GLU A 265 1 11 HELIX 7 AA7 SER A 273 THR A 286 1 14 HELIX 8 AA8 ASP A 294 ARG A 304 1 11 SHEET 1 AA1 5 MET A 116 VAL A 120 0 SHEET 2 AA1 5 LEU A 123 GLY A 126 -1 O LEU A 123 N VAL A 119 SHEET 3 AA1 5 GLY A 228 HIS A 232 1 O VAL A 231 N TRP A 124 SHEET 4 AA1 5 ILE A 142 ALA A 148 1 N LEU A 146 O LEU A 230 SHEET 5 AA1 5 ALA A 160 LEU A 164 1 O TYR A 162 N ILE A 145 CISPEP 1 ARG A 150 PRO A 151 0 -14.78 CRYST1 66.194 66.194 120.324 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 0.015107 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008311 0.00000