10 20 30 40 50 60 70 80 1WRM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 22-OCT-04 1WRM
TITLE CRYSTAL STRUCTURE OF JSP-1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PHOSPHATASE 22; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-163; COMPND 5 SYNONYM: LMW-DSP2, MITOGEN-ACTIVATED PROTEIN KINASE COMPND 6 PHOSPHATASE X, JNK-STIMULATING PHOSPHATASE 1; COMPND 7 EC: 3.1.3.48; 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE4)-RP; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32-A
KEYWDS PHOSPHATASE, DSP, JNK, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR T.YOKOTA,A.KASHIMA,R.KATO,S.SUGIO
REVDAT 3 24-FEB-09 1WRM 1 VERSN REVDAT 2 02-JAN-07 1WRM 1 JRNL REMARK REVDAT 1 22-OCT-05 1WRM 0
JRNL AUTH T.YOKOTA,Y.NARA,A.KASHIMA,K.MATSUBARA,S.MISAWA, JRNL AUTH 2 R.KATO,S.SUGIO JRNL TITL CRYSTAL STRUCTURE OF HUMAN DUAL SPECIFICITY JRNL TITL 2 PHOSPHATASE, JNK STIMULATORY PHOSPHATASE-1, AT 1.5 JRNL TITL 3 A RESOLUTION JRNL REF PROTEINS V. 66 272 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17068812 JRNL DOI 10.1002/PROT.21152
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2002 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1192695.440 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 23553 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1201 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 24754 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3022 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 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 : 1244 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.44000 REMARK 3 B22 (A**2) : -6.81000 REMARK 3 B33 (A**2) : 3.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -13.35000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.69 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.71 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP 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 : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 43.48 REMARK 3 REMARK 3 NCS MODEL : 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 : MES.PARAM 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 : MES.TOP REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WRM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-04. REMARK 100 THE RCSB ID CODE IS RCSB023919.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL24XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.83565 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, MAGNESIUM CHLORIDE, MES- REMARK 280 NAOH, PH 6.8, VAPOR DIFFUSION, TEMPERATURE 278K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 42.01350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.01350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.66000 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 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 GLY A 155 REMARK 465 GLU A 156 REMARK 465 SER A 157 REMARK 465 PRO A 158 REMARK 465 LEU A 159 REMARK 465 GLN A 160 REMARK 465 ASP A 161 REMARK 465 ALA A 162 REMARK 465 GLU A 163
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 MET A 44 -65.08 -122.63 REMARK 500 CYS A 88 -143.76 -131.44 REMARK 500 ASN A 126 86.82 -169.62 REMARK 500 GLU A 142 -32.10 -146.26 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 MES A 164
DBREF 1WRM A 1 163 UNP Q9NRW4 Q9NRW4_HUMAN 1 163
SEQADV 1WRM GLY A -2 UNP Q9NRW4 CLONING ARTIFACT SEQADV 1WRM PRO A -1 UNP Q9NRW4 CLONING ARTIFACT
SEQRES 1 A 165 GLY PRO MET GLY ASN GLY MET ASN LYS ILE LEU PRO GLY SEQRES 2 A 165 LEU TYR ILE GLY ASN PHE LYS ASP ALA ARG ASP ALA GLU SEQRES 3 A 165 GLN LEU SER LYS ASN LYS VAL THR HIS ILE LEU SER VAL SEQRES 4 A 165 HIS ASP SER ALA ARG PRO MET LEU GLU GLY VAL LYS TYR SEQRES 5 A 165 LEU CYS ILE PRO ALA ALA ASP SER PRO SER GLN ASN LEU SEQRES 6 A 165 THR ARG HIS PHE LYS GLU SER ILE LYS PHE ILE HIS GLU SEQRES 7 A 165 CYS ARG LEU ARG GLY GLU SER CYS LEU VAL HIS CYS LEU SEQRES 8 A 165 ALA GLY VAL SER ARG SER VAL THR LEU VAL ILE ALA TYR SEQRES 9 A 165 ILE MET THR VAL THR ASP PHE GLY TRP GLU ASP ALA LEU SEQRES 10 A 165 HIS THR VAL ARG ALA GLY ARG SER CYS ALA ASN PRO ASN SEQRES 11 A 165 VAL GLY PHE GLN ARG GLN LEU GLN GLU PHE GLU LYS HIS SEQRES 12 A 165 GLU VAL HIS GLN TYR ARG GLN TRP LEU LYS GLU GLU TYR SEQRES 13 A 165 GLY GLU SER PRO LEU GLN ASP ALA GLU
HET MES A 164 12
HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *80(H2 O)
HELIX 1 1 LYS A 18 ARG A 21 5 4 HELIX 2 2 ASP A 22 ASN A 29 1 8 HELIX 3 3 LEU A 63 ARG A 65 5 3 HELIX 4 4 HIS A 66 ARG A 80 1 15 HELIX 5 5 SER A 93 VAL A 106 1 14 HELIX 6 6 GLY A 110 ARG A 122 1 13 HELIX 7 7 ASN A 128 GLU A 142 1 15 HELIX 8 8 GLU A 142 TYR A 154 1 13
SHEET 1 A 5 ASN A 6 LEU A 9 0 SHEET 2 A 5 LEU A 12 GLY A 15 -1 O LEU A 12 N ILE A 8 SHEET 3 A 5 SER A 83 HIS A 87 1 O VAL A 86 N TYR A 13 SHEET 4 A 5 VAL A 31 SER A 36 1 N LEU A 35 O LEU A 85 SHEET 5 A 5 LYS A 49 CYS A 52 1 O LYS A 49 N THR A 32
SITE 1 AC1 12 LYS A 7 ILE A 8 LEU A 9 PRO A 10 SITE 2 AC1 12 ASP A 57 CYS A 88 LEU A 89 ALA A 90 SITE 3 AC1 12 GLY A 91 VAL A 92 SER A 93 ARG A 94
CRYST1 84.027 49.320 47.330 90.00 119.51 90.00 C 1 2 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 0.011901 0.000000 0.006736 0.00000
SCALE2 0.000000 0.020276 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024278 0.00000