PDB Short entry for 2IMG HEADER HYDROLASE 04-OCT-06 2IMG TITLE CRYSTAL STRUCTURE OF DUAL SPECIFICITY PROTEIN PHOSPHATASE TITLE 2 23 FROM HOMO SAPIENS IN COMPLEX WITH LIGAND MALATE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PROTEIN PHOSPHATASE 23; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LOW MOLECULAR MASS DUAL SPECIFICITY PHOSPHATASE 3, COMPND 5 LDP-3, VH1-LIKE PHOSPHATASE Z; COMPND 6 EC: 3.1.3.48, 3.1.3.16; COMPND 7 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: DUSP23; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSGX4 KEYWDS DUSP23, VHZ, LDP-3, DUAL SPECICITY PROTEIN PHOSPHATASE 23, KEYWDS 2 DUS23_HUMAN, MALATE, 8673A, STRUCTURAL GENOMICS, PSI, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER KEYWDS 4 FOR STRUCTURAL GENOMICS, NYSGXRC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.AGARWAL,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH AUTHOR 2 CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 3 21-OCT-08 2IMG 1 JRNL REVDAT 2 25-MAR-08 2IMG 1 VERSN REVDAT 1 17-OCT-06 2IMG 0 JRNL AUTH R.AGARWAL,S.K.BURLEY,S.SWAMINATHAN JRNL TITL STRUCTURE OF HUMAN DUAL SPECIFICITY PROTEIN JRNL TITL 2 PHOSPHATASE 23, VHZ, ENZYME-SUBSTRATE/PRODUCT JRNL TITL 3 COMPLEX. JRNL REF J.BIOL.CHEM. V. 283 8946 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18245086 JRNL DOI 10.1074/JBC.M708945200 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.93 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 96730.070 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 10835 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) : 0.195 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 324 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3071 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 96 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1161 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.98000 REMARK 3 B22 (A**2) : 6.74000 REMARK 3 B33 (A**2) : -4.76000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.83 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) : 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 : 0.34 REMARK 3 BSOL : 36.58 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : MLT-NEW.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : MLT-NEW.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE MISSING RESIDUES LISTED IN REMARK 3 REMARK 465 ARE DUE TO LACK OF ELECTRON DENSITY. REMARK 4 REMARK 4 2IMG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-06. REMARK 100 THE RCSB ID CODE IS RCSB039750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10874 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 33.800 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 19.00 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M DL MALIC ACID, 20% PEG 3350, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.98500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.62650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.62650 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 SER A 0 REMARK 465 LEU A 1 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 PRO A 13 117.16 -38.58 REMARK 500 ARG A 15 -46.82 -133.20 REMARK 500 ARG A 23 -1.94 -142.02 REMARK 500 CYS A 95 -146.36 -137.59 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 MLT A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-8673A RELATED DB: TARGETDB DBREF 2IMG A 2 150 UNP Q9BVJ7 DUS23_HUMAN 2 150 SEQADV 2IMG SER A 0 UNP Q9BVJ7 CLONING ARTIFACT SEQADV 2IMG LEU A 1 UNP Q9BVJ7 CLONING ARTIFACT SEQADV 2IMG MSE A 105 UNP Q9BVJ7 MET 105 MODIFIED RESIDUE SEQRES 1 A 151 SER LEU GLY VAL GLN PRO PRO ASN PHE SER TRP VAL LEU SEQRES 2 A 151 PRO GLY ARG LEU ALA GLY LEU ALA LEU PRO ARG LEU PRO SEQRES 3 A 151 ALA HIS TYR GLN PHE LEU LEU ASP LEU GLY VAL ARG HIS SEQRES 4 A 151 LEU VAL SER LEU THR GLU ARG GLY PRO PRO HIS SER ASP SEQRES 5 A 151 SER CYS PRO GLY LEU THR LEU HIS ARG LEU ARG ILE PRO SEQRES 6 A 151 ASP PHE CYS PRO PRO ALA PRO ASP GLN ILE ASP ARG PHE SEQRES 7 A 151 VAL GLN ILE VAL ASP GLU ALA ASN ALA ARG GLY GLU ALA SEQRES 8 A 151 VAL GLY VAL HIS CYS ALA LEU GLY PHE GLY ARG THR GLY SEQRES 9 A 151 THR MSE LEU ALA CYS TYR LEU VAL LYS GLU ARG GLY LEU SEQRES 10 A 151 ALA ALA GLY ASP ALA ILE ALA GLU ILE ARG ARG LEU ARG SEQRES 11 A 151 PRO GLY SER ILE GLU THR TYR GLU GLN GLU LYS ALA VAL SEQRES 12 A 151 PHE GLN PHE TYR GLN ARG THR LYS MODRES 2IMG MSE A 105 MET SELENOMETHIONINE HET MSE A 105 8 HET MLT A 501 9 HETNAM MSE SELENOMETHIONINE HETNAM MLT MALATE ION FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 MLT C4 H5 O5 1- FORMUL 3 HOH *114(H2 O) HELIX 1 1 LEU A 24 LEU A 34 1 11 HELIX 2 2 HIS A 49 CYS A 53 5 5 HELIX 3 3 ALA A 70 ARG A 87 1 18 HELIX 4 4 GLY A 100 GLY A 115 1 16 HELIX 5 5 ALA A 117 ARG A 129 1 13 HELIX 6 6 THR A 135 ARG A 148 1 14 SHEET 1 A 5 SER A 9 LEU A 12 0 SHEET 2 A 5 LEU A 16 LEU A 19 -1 O LEU A 16 N VAL A 11 SHEET 3 A 5 ALA A 90 HIS A 94 1 O VAL A 93 N ALA A 17 SHEET 4 A 5 VAL A 36 SER A 41 1 N VAL A 40 O GLY A 92 SHEET 5 A 5 THR A 57 ARG A 60 1 O HIS A 59 N LEU A 39 LINK C THR A 104 N MSE A 105 1555 1555 1.33 LINK C MSE A 105 N LEU A 106 1555 1555 1.32 SITE 1 AC1 11 PHE A 66 CYS A 95 ALA A 96 LEU A 97 SITE 2 AC1 11 GLY A 98 PHE A 99 GLY A 100 ARG A 101 SITE 3 AC1 11 TYR A 136 LYS A 140 HOH A 519 CRYST1 35.970 59.253 64.400 90.00 90.00 90.00 P 21 21 21 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 0.027801 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015528 0.00000