HEADER HYDROLASE 19-APR-12 4ERC TITLE STRUCTURE OF VHZ BOUND TO METAVANADATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PROTEIN PHOSPHATASE 23; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LOW MOLECULAR MASS DUAL SPECIFICITY PHOSPHATASE 3, LDP-3, COMPND 5 VH1-LIKE PHOSPHATASE Z; COMPND 6 EC: 3.1.3.16, 3.1.3.48; 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, LDP3, VHZ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 CODON+ (DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET45B(+) KEYWDS ALPHA BETA, PHOSPHATASE(HYDROLASE), HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.VYACHESLAV,C.H.ALVAN,J.J.SEAN REVDAT 3 28-FEB-24 4ERC 1 REMARK REVDAT 2 06-MAR-13 4ERC 1 JRNL REVDAT 1 19-DEC-12 4ERC 0 JRNL AUTH V.I.KUZNETSOV,A.C.HENGGE,S.J.JOHNSON JRNL TITL NEW ASPECTS OF THE PHOSPHATASE VHZ REVEALED BY A JRNL TITL 2 HIGH-RESOLUTION STRUCTURE WITH VANADATE AND SUBSTRATE JRNL TITL 3 SCREENING. JRNL REF BIOCHEMISTRY V. 51 9869 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 23145819 JRNL DOI 10.1021/BI300908Y REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 91098 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.3338 - 2.7682 0.97 6800 147 0.1609 0.1510 REMARK 3 2 2.7682 - 2.1974 1.00 6722 146 0.1281 0.1441 REMARK 3 3 2.1974 - 1.9196 1.00 6691 145 0.1138 0.1314 REMARK 3 4 1.9196 - 1.7441 0.98 6543 145 0.1165 0.1256 REMARK 3 5 1.7441 - 1.6191 0.99 6545 144 0.1043 0.1502 REMARK 3 6 1.6191 - 1.5237 0.98 6483 141 0.0995 0.1274 REMARK 3 7 1.5237 - 1.4474 0.98 6435 138 0.1033 0.1445 REMARK 3 8 1.4474 - 1.3844 0.97 6369 141 0.1034 0.1396 REMARK 3 9 1.3844 - 1.3311 0.96 6304 138 0.1036 0.1441 REMARK 3 10 1.3311 - 1.2851 0.95 6291 137 0.1067 0.1300 REMARK 3 11 1.2851 - 1.2450 0.94 6180 135 0.1124 0.1581 REMARK 3 12 1.2450 - 1.2094 0.93 6057 131 0.1208 0.1634 REMARK 3 13 1.2094 - 1.1775 0.92 5976 131 0.1359 0.1599 REMARK 3 14 1.1775 - 1.1488 0.87 5761 122 0.1650 0.2133 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 70.89 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.060 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) : 1.12090 REMARK 3 B22 (A**2) : -1.37880 REMARK 3 B33 (A**2) : 0.25790 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2478 REMARK 3 ANGLE : 1.245 3377 REMARK 3 CHIRALITY : 0.067 362 REMARK 3 PLANARITY : 0.007 456 REMARK 3 DIHEDRAL : 12.691 948 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ERC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000071973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI 111 DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94449 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : 0.66600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VHZ 20 MG/ML IN THE CRYSTALLIZATION REMARK 280 BUFFER WAS MIXED WITH 50 MM SOLUTION OF SODIUM VANADATE (FINAL REMARK 280 VANADATE CONCENTRATION 10MM ONE UL OF PROTEIN-VANADATE COMPLEX REMARK 280 WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONTAINING 150 REMARK 280 MM L-MALATE, PH 7.0 AND PEG3350 (15-20 % V/W), VAPOR DIFFUSION, REMARK 280 TEMPERATURE 298K, PH 7.5 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 16.49600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.85900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.85900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.49600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.98500 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ARG A 23 13.52 -159.06 REMARK 500 CYS A 95 -148.02 -129.56 REMARK 500 ILE A 133 92.20 65.90 REMARK 500 ARG B 15 -45.97 -134.52 REMARK 500 ALA B 20 -166.46 -78.99 REMARK 500 ARG B 23 0.41 -151.54 REMARK 500 CYS B 95 -149.68 -127.89 REMARK 500 ILE B 133 99.27 69.10 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 VN4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VN4 B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IMG RELATED DB: PDB REMARK 900 VHZ COMPLEXED WITH MALATE INHIBITOR DBREF 4ERC A 1 150 UNP Q9BVJ7 DUS23_HUMAN 1 150 DBREF 4ERC B 1 150 UNP Q9BVJ7 DUS23_HUMAN 1 150 SEQRES 1 A 150 MET GLY VAL GLN PRO PRO ASN PHE SER TRP VAL LEU PRO SEQRES 2 A 150 GLY ARG LEU ALA GLY LEU ALA LEU PRO ARG LEU PRO ALA SEQRES 3 A 150 HIS TYR GLN PHE LEU LEU ASP LEU GLY VAL ARG HIS LEU SEQRES 4 A 150 VAL SER LEU THR GLU ARG GLY PRO PRO HIS SER ASP SER SEQRES 5 A 150 CYS PRO GLY LEU THR LEU HIS ARG LEU ARG ILE PRO ASP SEQRES 6 A 150 PHE CYS PRO PRO ALA PRO ASP GLN ILE ASP ARG PHE VAL SEQRES 7 A 150 GLN ILE VAL ASP GLU ALA ASN ALA ARG GLY GLU ALA VAL SEQRES 8 A 150 GLY VAL HIS CYS ALA LEU GLY PHE GLY ARG THR GLY THR SEQRES 9 A 150 MET LEU ALA CYS TYR LEU VAL LYS GLU ARG GLY LEU ALA SEQRES 10 A 150 ALA GLY ASP ALA ILE ALA GLU ILE ARG ARG LEU ARG PRO SEQRES 11 A 150 GLY SER ILE GLU THR TYR GLU GLN GLU LYS ALA VAL PHE SEQRES 12 A 150 GLN PHE TYR GLN ARG THR LYS SEQRES 1 B 150 MET GLY VAL GLN PRO PRO ASN PHE SER TRP VAL LEU PRO SEQRES 2 B 150 GLY ARG LEU ALA GLY LEU ALA LEU PRO ARG LEU PRO ALA SEQRES 3 B 150 HIS TYR GLN PHE LEU LEU ASP LEU GLY VAL ARG HIS LEU SEQRES 4 B 150 VAL SER LEU THR GLU ARG GLY PRO PRO HIS SER ASP SER SEQRES 5 B 150 CYS PRO GLY LEU THR LEU HIS ARG LEU ARG ILE PRO ASP SEQRES 6 B 150 PHE CYS PRO PRO ALA PRO ASP GLN ILE ASP ARG PHE VAL SEQRES 7 B 150 GLN ILE VAL ASP GLU ALA ASN ALA ARG GLY GLU ALA VAL SEQRES 8 B 150 GLY VAL HIS CYS ALA LEU GLY PHE GLY ARG THR GLY THR SEQRES 9 B 150 MET LEU ALA CYS TYR LEU VAL LYS GLU ARG GLY LEU ALA SEQRES 10 B 150 ALA GLY ASP ALA ILE ALA GLU ILE ARG ARG LEU ARG PRO SEQRES 11 B 150 GLY SER ILE GLU THR TYR GLU GLN GLU LYS ALA VAL PHE SEQRES 12 B 150 GLN PHE TYR GLN ARG THR LYS HET VN4 A 201 4 HET VN4 B 201 4 HETNAM VN4 OXIDO(DIOXO)VANADIUM FORMUL 3 VN4 2(O3 V 1-) FORMUL 5 HOH *439(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 PHE A 99 GLY A 115 1 17 HELIX 5 5 ALA A 117 ARG A 129 1 13 HELIX 6 6 THR A 135 LYS A 150 1 16 HELIX 7 7 LEU B 24 LEU B 34 1 11 HELIX 8 8 HIS B 49 CYS B 53 5 5 HELIX 9 9 ALA B 70 ARG B 87 1 18 HELIX 10 10 PHE B 99 GLY B 115 1 17 HELIX 11 11 ALA B 117 ARG B 129 1 13 HELIX 12 12 THR B 135 LYS B 150 1 16 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 91 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 THR A 57 N LEU A 39 SHEET 1 B 5 SER B 9 LEU B 12 0 SHEET 2 B 5 LEU B 16 LEU B 19 -1 O LEU B 16 N LEU B 12 SHEET 3 B 5 ALA B 90 HIS B 94 1 O VAL B 91 N ALA B 17 SHEET 4 B 5 VAL B 36 SER B 41 1 N VAL B 40 O GLY B 92 SHEET 5 B 5 THR B 57 ARG B 60 1 O HIS B 59 N SER B 41 SITE 1 AC1 11 ARG A 60 ASP A 65 CYS A 95 ALA A 96 SITE 2 AC1 11 LEU A 97 GLY A 98 PHE A 99 GLY A 100 SITE 3 AC1 11 ARG A 101 GLU A 134 HOH A 302 SITE 1 AC2 11 ASP B 65 CYS B 95 ALA B 96 LEU B 97 SITE 2 AC2 11 GLY B 98 PHE B 99 GLY B 100 ARG B 101 SITE 3 AC2 11 GLU B 134 HOH B 368 HOH B 422 CRYST1 32.992 79.970 99.718 90.00 90.00 90.00 P 21 21 21 8 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 0.030310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012505 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010028 0.00000