HEADER HYDROLASE 14-JUN-05 1ZZW TITLE CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN MAP KINASE PHOSPHATASE TITLE 2 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PROTEIN PHOSPHATASE 10; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PHOSPHATASE, MKP, PTP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.G.JEONG,T.S.YOON,J.H.KIM,M.Y.SHIM,S.K.JEONG,J.H.SON,S.E.RYU,S.J.KIM REVDAT 4 13-MAR-24 1ZZW 1 REMARK SEQADV REVDAT 3 24-FEB-09 1ZZW 1 VERSN REVDAT 2 08-AUG-06 1ZZW 1 JRNL REVDAT 1 04-JUL-06 1ZZW 0 JRNL AUTH D.G.JEONG,T.S.YOON,J.H.KIM,M.Y.SHIM,S.K.JEONG,J.H.SON, JRNL AUTH 2 S.E.RYU,S.J.KIM JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN MAP JRNL TITL 2 KINASE PHOSPHATASE 5: STRUCTURAL INSIGHT INTO CONSTITUTIVELY JRNL TITL 3 ACTIVE PHOSPHATASE. JRNL REF J.MOL.BIOL. V. 360 946 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16806267 JRNL DOI 10.1016/J.JMB.2006.05.059 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 37891 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1890 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2384 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37893 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, LITHIUM SULFATE, MAGNESIUM REMARK 280 SULFATE, DTT, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 VAL A 466 REMARK 465 THR A 467 REMARK 465 MET B 319 REMARK 465 ALA B 320 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 VAL A 354 59.39 -95.19 REMARK 500 PRO A 374 69.81 -69.38 REMARK 500 ASP A 377 36.80 -99.57 REMARK 500 CYS A 408 -136.32 -135.06 REMARK 500 SER A 446 73.84 -163.25 REMARK 500 VAL B 354 51.01 -92.42 REMARK 500 PRO B 374 59.65 -65.91 REMARK 500 THR B 376 -168.26 -103.30 REMARK 500 CYS B 408 -119.42 -139.59 REMARK 500 VAL B 412 33.62 35.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 503 DBREF 1ZZW A 320 467 UNP Q9Y6W6 DUS10_HUMAN 320 467 DBREF 1ZZW B 320 467 UNP Q9Y6W6 DUS10_HUMAN 320 467 SEQADV 1ZZW MET A 319 UNP Q9Y6W6 INITIATING METHIONINE SEQADV 1ZZW MET B 319 UNP Q9Y6W6 INITIATING METHIONINE SEQRES 1 A 149 MET ALA GLU LEU THR PRO ILE LEU PRO PHE LEU PHE LEU SEQRES 2 A 149 GLY ASN GLU GLN ASP ALA GLN ASP LEU ASP THR MET GLN SEQRES 3 A 149 ARG LEU ASN ILE GLY TYR VAL ILE ASN VAL THR THR HIS SEQRES 4 A 149 LEU PRO LEU TYR HIS TYR GLU LYS GLY LEU PHE ASN TYR SEQRES 5 A 149 LYS ARG LEU PRO ALA THR ASP SER ASN LYS GLN ASN LEU SEQRES 6 A 149 ARG GLN TYR PHE GLU GLU ALA PHE GLU PHE ILE GLU GLU SEQRES 7 A 149 ALA HIS GLN CYS GLY LYS GLY LEU LEU ILE HIS CYS GLN SEQRES 8 A 149 ALA GLY VAL SER ARG SER ALA THR ILE VAL ILE ALA TYR SEQRES 9 A 149 LEU MET LYS HIS THR ARG MET THR MET THR ASP ALA TYR SEQRES 10 A 149 LYS PHE VAL LYS GLY LYS ARG PRO ILE ILE SER PRO ASN SEQRES 11 A 149 LEU ASN PHE MET GLY GLN LEU LEU GLU PHE GLU GLU ASP SEQRES 12 A 149 LEU ASN ASN GLY VAL THR SEQRES 1 B 149 MET ALA GLU LEU THR PRO ILE LEU PRO PHE LEU PHE LEU SEQRES 2 B 149 GLY ASN GLU GLN ASP ALA GLN ASP LEU ASP THR MET GLN SEQRES 3 B 149 ARG LEU ASN ILE GLY TYR VAL ILE ASN VAL THR THR HIS SEQRES 4 B 149 LEU PRO LEU TYR HIS TYR GLU LYS GLY LEU PHE ASN TYR SEQRES 5 B 149 LYS ARG LEU PRO ALA THR ASP SER ASN LYS GLN ASN LEU SEQRES 6 B 149 ARG GLN TYR PHE GLU GLU ALA PHE GLU PHE ILE GLU GLU SEQRES 7 B 149 ALA HIS GLN CYS GLY LYS GLY LEU LEU ILE HIS CYS GLN SEQRES 8 B 149 ALA GLY VAL SER ARG SER ALA THR ILE VAL ILE ALA TYR SEQRES 9 B 149 LEU MET LYS HIS THR ARG MET THR MET THR ASP ALA TYR SEQRES 10 B 149 LYS PHE VAL LYS GLY LYS ARG PRO ILE ILE SER PRO ASN SEQRES 11 B 149 LEU ASN PHE MET GLY GLN LEU LEU GLU PHE GLU GLU ASP SEQRES 12 B 149 LEU ASN ASN GLY VAL THR HET SO4 A 501 5 HET SO4 B 502 5 HET EDO B 503 4 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *263(H2 O) HELIX 1 1 GLN A 335 GLN A 338 5 4 HELIX 2 2 ASP A 339 LEU A 346 1 8 HELIX 3 3 HIS A 362 GLY A 366 5 5 HELIX 4 4 LEU A 383 GLN A 385 5 3 HELIX 5 5 TYR A 386 CYS A 400 1 15 HELIX 6 6 SER A 413 THR A 427 1 15 HELIX 7 7 THR A 430 ARG A 442 1 13 HELIX 8 8 ASN A 448 ASN A 464 1 17 HELIX 9 9 GLN B 335 GLN B 338 5 4 HELIX 10 10 ASP B 339 LEU B 346 1 8 HELIX 11 11 HIS B 362 GLY B 366 5 5 HELIX 12 12 LEU B 383 GLN B 385 5 3 HELIX 13 13 TYR B 386 CYS B 400 1 15 HELIX 14 14 VAL B 412 THR B 427 1 16 HELIX 15 15 THR B 430 ARG B 442 1 13 HELIX 16 16 ASN B 448 ASN B 464 1 17 SHEET 1 A 5 THR A 323 LEU A 326 0 SHEET 2 A 5 LEU A 329 GLY A 332 -1 O LEU A 329 N ILE A 325 SHEET 3 A 5 GLY A 403 HIS A 407 1 O ILE A 406 N PHE A 330 SHEET 4 A 5 ILE A 348 ASN A 353 1 N ILE A 352 O LEU A 405 SHEET 5 A 5 ASN A 369 ARG A 372 1 O ASN A 369 N VAL A 351 SHEET 1 B 5 THR B 323 LEU B 326 0 SHEET 2 B 5 LEU B 329 GLY B 332 -1 O LEU B 329 N ILE B 325 SHEET 3 B 5 GLY B 403 HIS B 407 1 O LEU B 404 N PHE B 330 SHEET 4 B 5 ILE B 348 ASN B 353 1 N ILE B 352 O LEU B 405 SHEET 5 B 5 ASN B 369 ARG B 372 1 O ASN B 369 N VAL B 351 SITE 1 AC1 8 ASP A 377 CYS A 408 GLN A 409 ALA A 410 SITE 2 AC1 8 GLY A 411 VAL A 412 SER A 413 ARG A 414 SITE 1 AC2 8 HOH B 226 CYS B 408 GLN B 409 ALA B 410 SITE 2 AC2 8 GLY B 411 VAL B 412 SER B 413 ARG B 414 SITE 1 AC3 7 HOH B 255 SER B 413 THR B 417 ILE B 445 SITE 2 AC3 7 SER B 446 ASN B 448 PHE B 451 CRYST1 39.533 41.073 55.569 95.35 99.81 117.35 P 1 2 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 0.025295 0.013084 0.007075 0.00000 SCALE2 0.000000 0.027411 0.005478 0.00000 SCALE3 0.000000 0.000000 0.018624 0.00000