HEADER HYDROLASE 10-FEB-07 2OUC TITLE CRYSTAL STRUCTURE OF THE MAP KINASE BINDING DOMAIN OF MKP5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PROTEIN PHOSPHATASE 10; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RHODANESE DOMAIN (RESIDUES 148-287); COMPND 5 SYNONYM: MITOGEN-ACTIVATED PROTEIN KINASE PHOSPHATASE 5, MAP KINASE COMPND 6 PHOSPHATASE 5, MKP-5; COMPND 7 EC: 3.1.3.48, 3.1.3.16; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MKP5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RHODANESE FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.TAO,L.TONG REVDAT 4 21-FEB-24 2OUC 1 SEQADV REVDAT 3 18-OCT-17 2OUC 1 REMARK REVDAT 2 24-FEB-09 2OUC 1 VERSN REVDAT 1 07-AUG-07 2OUC 0 JRNL AUTH X.TAO,L.TONG JRNL TITL CRYSTAL STRUCTURE OF THE MAP KINASE BINDING DOMAIN AND THE JRNL TITL 2 CATALYTIC DOMAIN OF HUMAN MKP5. JRNL REF PROTEIN SCI. V. 16 880 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17400920 JRNL DOI 10.1110/PS.062712807 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 579830.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 28451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2726 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2021 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 233 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2126 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.34000 REMARK 3 B22 (A**2) : 8.63000 REMARK 3 B33 (A**2) : -11.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.470 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.400 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.450 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 54.53 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OUC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041595. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31415 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1234 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.411 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SNB THEN SOLVE/RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE (PH 4.5), AND REMARK 280 2.3-2.5 M AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.08200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 CYS A 162 REMARK 465 SER A 163 REMARK 465 LYS A 164 REMARK 465 SER A 165 REMARK 465 HIS A 166 REMARK 465 LEU A 167 REMARK 465 PRO A 168 REMARK 465 SER A 169 REMARK 465 GLN A 170 REMARK 465 GLY A 171 REMARK 465 CYS B 162 REMARK 465 SER B 163 REMARK 465 LYS B 164 REMARK 465 SER B 165 REMARK 465 HIS B 166 REMARK 465 LEU B 167 REMARK 465 PRO B 168 REMARK 465 SER B 169 REMARK 465 GLN B 170 REMARK 465 GLY B 171 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 186 141.07 -170.13 REMARK 500 CYS A 218 1.71 -62.92 REMARK 500 GLU A 220 -131.13 -99.89 REMARK 500 LYS A 222 -68.04 -26.25 REMARK 500 ASP A 237 -160.83 -106.02 REMARK 500 ASN A 239 16.16 -165.14 REMARK 500 SER B 186 149.33 -174.02 REMARK 500 GLN B 207 -108.05 -89.37 REMARK 500 GLU B 220 -136.61 -99.65 REMARK 500 LYS B 222 -91.39 -38.98 REMARK 500 ASP B 237 -162.37 -123.72 REMARK 500 ASN B 239 1.94 -163.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OUD RELATED DB: PDB DBREF 2OUC A 148 287 UNP Q9Y6W6 DUS10_HUMAN 148 287 DBREF 2OUC B 148 287 UNP Q9Y6W6 DUS10_HUMAN 148 287 SEQADV 2OUC LYS A 288 UNP Q9Y6W6 CLONING ARTIFACT SEQADV 2OUC GLU A 289 UNP Q9Y6W6 CLONING ARTIFACT SEQADV 2OUC LYS B 288 UNP Q9Y6W6 CLONING ARTIFACT SEQADV 2OUC GLU B 289 UNP Q9Y6W6 CLONING ARTIFACT SEQRES 1 A 142 LYS ILE ILE TYR PRO ASN ASP LEU ALA LYS LYS MET THR SEQRES 2 A 142 LYS CYS SER LYS SER HIS LEU PRO SER GLN GLY PRO VAL SEQRES 3 A 142 ILE ILE ASP CYS ARG PRO PHE MET GLU TYR ASN LYS SER SEQRES 4 A 142 HIS ILE GLN GLY ALA VAL HIS ILE ASN CYS ALA ASP LYS SEQRES 5 A 142 ILE SER ARG ARG ARG LEU GLN GLN GLY LYS ILE THR VAL SEQRES 6 A 142 LEU ASP LEU ILE SER CYS ARG GLU GLY LYS ASP SER PHE SEQRES 7 A 142 LYS ARG ILE PHE SER LYS GLU ILE ILE VAL TYR ASP GLU SEQRES 8 A 142 ASN THR ASN GLU PRO SER ARG VAL MET PRO SER GLN PRO SEQRES 9 A 142 LEU HIS ILE VAL LEU GLU SER LEU LYS ARG GLU GLY LYS SEQRES 10 A 142 GLU PRO LEU VAL LEU LYS GLY GLY LEU SER SER PHE LYS SEQRES 11 A 142 GLN ASN HIS GLU ASN LEU CYS ASP ASN SER LYS GLU SEQRES 1 B 142 LYS ILE ILE TYR PRO ASN ASP LEU ALA LYS LYS MET THR SEQRES 2 B 142 LYS CYS SER LYS SER HIS LEU PRO SER GLN GLY PRO VAL SEQRES 3 B 142 ILE ILE ASP CYS ARG PRO PHE MET GLU TYR ASN LYS SER SEQRES 4 B 142 HIS ILE GLN GLY ALA VAL HIS ILE ASN CYS ALA ASP LYS SEQRES 5 B 142 ILE SER ARG ARG ARG LEU GLN GLN GLY LYS ILE THR VAL SEQRES 6 B 142 LEU ASP LEU ILE SER CYS ARG GLU GLY LYS ASP SER PHE SEQRES 7 B 142 LYS ARG ILE PHE SER LYS GLU ILE ILE VAL TYR ASP GLU SEQRES 8 B 142 ASN THR ASN GLU PRO SER ARG VAL MET PRO SER GLN PRO SEQRES 9 B 142 LEU HIS ILE VAL LEU GLU SER LEU LYS ARG GLU GLY LYS SEQRES 10 B 142 GLU PRO LEU VAL LEU LYS GLY GLY LEU SER SER PHE LYS SEQRES 11 B 142 GLN ASN HIS GLU ASN LEU CYS ASP ASN SER LYS GLU FORMUL 3 HOH *115(H2 O) HELIX 1 1 TYR A 151 LYS A 161 1 11 HELIX 2 2 PRO A 179 LYS A 185 1 7 HELIX 3 3 ASP A 198 GLN A 207 1 10 HELIX 4 4 THR A 211 CYS A 218 1 8 HELIX 5 5 ASP A 223 LYS A 231 1 9 HELIX 6 6 GLU A 242 VAL A 246 5 5 HELIX 7 7 GLN A 250 GLU A 262 1 13 HELIX 8 8 GLY A 271 LYS A 277 1 7 HELIX 9 9 GLN A 278 ASN A 279 5 2 HELIX 10 10 HIS A 280 ASN A 282 5 3 HELIX 11 11 TYR B 151 THR B 160 1 10 HELIX 12 12 PRO B 179 LYS B 185 1 7 HELIX 13 13 ASP B 198 GLN B 207 1 10 HELIX 14 14 THR B 211 CYS B 218 1 8 HELIX 15 15 ASP B 223 PHE B 229 1 7 HELIX 16 16 GLU B 242 VAL B 246 5 5 HELIX 17 17 GLN B 250 GLU B 262 1 13 HELIX 18 18 GLY B 271 GLU B 281 1 11 SHEET 1 A 5 ILE A 149 ILE A 150 0 SHEET 2 A 5 LEU A 267 LEU A 269 1 O VAL A 268 N ILE A 150 SHEET 3 A 5 ILE A 233 TYR A 236 1 N VAL A 235 O LEU A 267 SHEET 4 A 5 VAL A 173 ASP A 176 1 N VAL A 173 O ILE A 234 SHEET 5 A 5 VAL A 192 HIS A 193 1 O VAL A 192 N ILE A 174 SHEET 1 B 2 SER A 186 ILE A 188 0 SHEET 2 B 2 CYS A 284 ASN A 286 -1 O ASP A 285 N HIS A 187 SHEET 1 C 5 ILE B 149 ILE B 150 0 SHEET 2 C 5 LEU B 267 LEU B 269 1 O VAL B 268 N ILE B 150 SHEET 3 C 5 ILE B 233 TYR B 236 1 N VAL B 235 O LEU B 267 SHEET 4 C 5 VAL B 173 ASP B 176 1 N VAL B 173 O ILE B 234 SHEET 5 C 5 VAL B 192 HIS B 193 1 O VAL B 192 N ILE B 174 SHEET 1 D 2 SER B 186 ILE B 188 0 SHEET 2 D 2 CYS B 284 ASN B 286 -1 O ASP B 285 N HIS B 187 CRYST1 49.296 52.164 62.267 90.00 89.36 90.00 P 1 21 1 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 0.020286 0.000000 -0.000228 0.00000 SCALE2 0.000000 0.019170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016061 0.00000