HEADER HYDROLASE 03-AUG-06 2HXP TITLE CRYSTAL STRUCTURE OF THE HUMAN PHOSPHATASE (DUSP9) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PROTEIN PHOSPHATASE 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 201-345; COMPND 5 EC: 3.1.3.48; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DUSP9, MKP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 8638A, HUMAN PHOSPHATASE, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, NYSGXRC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.MADEGOWDA,S.ESWARAMOORTHY,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 5 14-FEB-24 2HXP 1 REMARK REVDAT 4 20-OCT-21 2HXP 1 SEQADV REVDAT 3 03-FEB-21 2HXP 1 AUTHOR JRNL REMARK SEQADV REVDAT 2 25-MAR-08 2HXP 1 JRNL VERSN REVDAT 1 22-AUG-06 2HXP 0 JRNL AUTH S.C.ALMO,J.B.BONANNO,J.M.SAUDER,S.EMTAGE,T.P.DILORENZO, JRNL AUTH 2 V.MALASHKEVICH,S.R.WASSERMAN,S.SWAMINATHAN,S.ESWARAMOORTHY, JRNL AUTH 3 R.AGARWAL,D.KUMARAN,M.MADEGOWDA,S.RAGUMANI,Y.PATSKOVSKY, JRNL AUTH 4 J.ALVARADO,U.A.RAMAGOPAL,J.FABER-BARATA,M.R.CHANCE,A.SALI, JRNL AUTH 5 A.FISER,Z.Y.ZHANG,D.S.LAWRENCE,S.K.BURLEY JRNL TITL STRUCTURAL GENOMICS OF PROTEIN PHOSPHATASES. JRNL REF J.STRUCT.FUNCT.GENOM. V. 8 121 2007 JRNL REFN ISSN 1345-711X JRNL PMID 18058037 JRNL DOI 10.1007/S10969-007-9036-1 REMARK 2 REMARK 2 RESOLUTION. 1.83 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 270810.070 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 14920 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) : 0.216 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 744 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2311 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 119 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1157 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -1.91000 REMARK 3 B12 (A**2) : 2.06000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.920 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) : 1.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.940 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 46.33 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 : CARBOHYDRATE.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 : CARBOHYDRATE.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: RESIDUES LISTED IN REMARK 465 WERE NOT REMARK 3 MODELED DUE TO LACK OF OR WEAK ELECTRON DENSITY. THE RESIDUAL REMARK 3 DENSITY WAS MODELED AS PHOSPHATE, HOWEVER IT COULD EQUALLY WELL REMARK 3 BE SULFATE. REMARK 4 REMARK 4 2HXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000038883. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1, 1.7 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14920 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 24.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.02200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M BIS-TRIS, 0.2M REMARK 280 AMMONIUM SULPHATE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.90067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.95033 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 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 SER A 199 REMARK 465 LEU A 200 REMARK 465 ALA A 201 REMARK 465 GLU A 346 REMARK 465 GLY A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 REMARK 465 HIS A 350 REMARK 465 HIS A 351 REMARK 465 HIS A 352 REMARK 465 HIS A 353 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 ASN A 210 -1.76 78.22 REMARK 500 VAL A 236 55.40 -94.40 REMARK 500 PRO A 256 60.23 -69.52 REMARK 500 SER A 290 -143.20 -136.63 REMARK 500 LEU A 291 -83.28 -84.74 REMARK 500 SER A 295 -64.47 -144.49 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 PO4 A 354 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-8638A RELATED DB: TARGETDB DBREF 2HXP A 201 345 UNP Q99956 DUS9_HUMAN 201 345 SEQADV 2HXP SER A 199 UNP Q99956 EXPRESSION TAG SEQADV 2HXP LEU A 200 UNP Q99956 EXPRESSION TAG SEQADV 2HXP SER A 290 UNP Q99956 CYS 290 ENGINEERED MUTATION SEQADV 2HXP GLU A 346 UNP Q99956 EXPRESSION TAG SEQADV 2HXP GLY A 347 UNP Q99956 EXPRESSION TAG SEQADV 2HXP HIS A 348 UNP Q99956 EXPRESSION TAG SEQADV 2HXP HIS A 349 UNP Q99956 EXPRESSION TAG SEQADV 2HXP HIS A 350 UNP Q99956 EXPRESSION TAG SEQADV 2HXP HIS A 351 UNP Q99956 EXPRESSION TAG SEQADV 2HXP HIS A 352 UNP Q99956 EXPRESSION TAG SEQADV 2HXP HIS A 353 UNP Q99956 EXPRESSION TAG SEQRES 1 A 155 SER LEU ALA SER PHE PRO VAL GLN ILE LEU PRO ASN LEU SEQRES 2 A 155 TYR LEU GLY SER ALA ARG ASP SER ALA ASN LEU GLU SER SEQRES 3 A 155 LEU ALA LYS LEU GLY ILE ARG TYR ILE LEU ASN VAL THR SEQRES 4 A 155 PRO ASN LEU PRO ASN PHE PHE GLU LYS ASN GLY ASP PHE SEQRES 5 A 155 HIS TYR LYS GLN ILE PRO ILE SER ASP HIS TRP SER GLN SEQRES 6 A 155 ASN LEU SER ARG PHE PHE PRO GLU ALA ILE GLU PHE ILE SEQRES 7 A 155 ASP GLU ALA LEU SER GLN ASN CYS GLY VAL LEU VAL HIS SEQRES 8 A 155 SER LEU ALA GLY VAL SER ARG SER VAL THR VAL THR VAL SEQRES 9 A 155 ALA TYR LEU MET GLN LYS LEU HIS LEU SER LEU ASN ASP SEQRES 10 A 155 ALA TYR ASP LEU VAL LYS ARG LYS LYS SER ASN ILE SER SEQRES 11 A 155 PRO ASN PHE ASN PHE MET GLY GLN LEU LEU ASP PHE GLU SEQRES 12 A 155 ARG SER LEU ARG GLU GLY HIS HIS HIS HIS HIS HIS HET PO4 A 354 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *100(H2 O) HELIX 1 1 ARG A 217 ALA A 220 5 4 HELIX 2 2 ASN A 221 LEU A 228 1 8 HELIX 3 3 SER A 258 GLN A 263 5 6 HELIX 4 4 ASN A 264 GLN A 282 1 19 HELIX 5 5 SER A 295 HIS A 310 1 16 HELIX 6 6 SER A 312 LYS A 324 1 13 HELIX 7 7 ASN A 330 ARG A 345 1 16 SHEET 1 A 5 VAL A 205 LEU A 208 0 SHEET 2 A 5 LEU A 211 GLY A 214 -1 O LEU A 211 N LEU A 208 SHEET 3 A 5 GLY A 285 HIS A 289 1 O VAL A 288 N GLY A 214 SHEET 4 A 5 ILE A 230 ASN A 235 1 N LEU A 234 O LEU A 287 SHEET 5 A 5 HIS A 251 GLN A 254 1 O HIS A 251 N ARG A 231 SITE 1 AC1 8 SER A 290 LEU A 291 ALA A 292 GLY A 293 SITE 2 AC1 8 VAL A 294 SER A 295 ARG A 296 HOH A 426 CRYST1 50.527 50.527 59.851 90.00 90.00 120.00 P 32 3 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 0.019791 0.011427 0.000000 0.00000 SCALE2 0.000000 0.022853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016708 0.00000