HEADER HYDROLASE 31-JUL-03 1UJC TITLE STRUCTURE OF THE PROTEIN HISTIDINE PHOSPHATASE SIXA COMPLEXED WITH TITLE 2 TUNGSTATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOHISTIDINE PHOSPHATASE SIXA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HISTIDINE PHOSPHATASE SIXA, RX6; COMPND 5 EC: 3.1.3.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ALPHA-BETA FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.HAMADA,M.KATO,T.SHIMIZU,K.IHARA,T.MIZUNO,T.HAKOSHIMA REVDAT 3 27-DEC-23 1UJC 1 REMARK LINK REVDAT 2 24-FEB-09 1UJC 1 VERSN REVDAT 1 25-JAN-05 1UJC 0 JRNL AUTH K.HAMADA,M.KATO,T.SHIMIZU,K.IHARA,T.MIZUNO,T.HAKOSHIMA JRNL TITL CRYSTAL STRUCTURE OF THE PROTEIN HISTIDINE PHOSPHATASE SIXA JRNL TITL 2 IN THE MULTISTEP HIS-ASP PHOSPHORELAY. JRNL REF GENES CELLS V. 10 1 2005 JRNL REFN ISSN 1356-9597 JRNL PMID 15670209 JRNL DOI 10.1111/J.1365-2443.2005.00817.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.HAMADA,M.KATO,T.MIZUNO,T.HAKOSHIMA REMARK 1 TITL CRYSTALLOGRAPHIC CHARACTERIZATION OF A NOVEL PROTEIN SIXA REMARK 1 TITL 2 WHICH EXHIBITS PHOSPHO-HISTIDINE PHOSPHATASE ACTIVITY IN THE REMARK 1 TITL 3 MULTISTEP HIS-ASP PHOSPHORELAY REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 269 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1087869.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 11829 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) : 0.199 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1218 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1394 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 148 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1165 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -2.09000 REMARK 3 B33 (A**2) : 2.50000 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) : 0.12 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 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) : 1.070 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.510 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 14.350; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 12.590; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 36.54 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000005888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12302 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 36.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, CACL2, MES, WO4NA2, PH 6.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K 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 19.56300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.98150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.86850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.98150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.56300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.86850 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 MET A 157 REMARK 465 ALA A 158 REMARK 465 LYS A 159 REMARK 465 ALA A 160 REMARK 465 ILE A 161 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 SER A 107 -147.45 -144.76 REMARK 500 SER A 131 -2.93 71.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 WO4 A 163 W REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 8 NE2 REMARK 620 2 WO4 A 163 O1 80.6 REMARK 620 3 WO4 A 163 O2 69.5 109.9 REMARK 620 4 WO4 A 163 O3 68.8 111.3 113.7 REMARK 620 5 WO4 A 163 O4 170.9 108.5 106.6 106.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 162 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 65 O REMARK 620 2 GLY A 99 O 137.3 REMARK 620 3 HOH A 297 O 75.2 147.3 REMARK 620 4 HOH A 401 O 73.8 63.7 147.3 REMARK 620 5 HOH A 402 O 77.2 91.6 101.5 81.7 REMARK 620 6 HOH A 403 O 82.8 100.4 77.0 88.8 159.6 REMARK 620 7 HOH A 404 O 129.7 89.2 59.4 140.7 129.5 67.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WO4 A 163 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UJB RELATED DB: PDB REMARK 900 1UJB CONTAINS THE SAME PROTEIN IN THE APO FORM. DBREF 1UJC A 1 161 UNP P76502 SIXA_ECOLI 1 161 SEQRES 1 A 161 MET GLN VAL PHE ILE MET ARG HIS GLY ASP ALA ALA LEU SEQRES 2 A 161 ASP ALA ALA SER ASP SER VAL ARG PRO LEU THR THR ASN SEQRES 3 A 161 GLY CYS ASP GLU SER ARG LEU MET ALA ASN TRP LEU LYS SEQRES 4 A 161 GLY GLN LYS VAL GLU ILE GLU ARG VAL LEU VAL SER PRO SEQRES 5 A 161 PHE LEU ARG ALA GLU GLN THR LEU GLU GLU VAL GLY ASP SEQRES 6 A 161 CYS LEU ASN LEU PRO SER SER ALA GLU VAL LEU PRO GLU SEQRES 7 A 161 LEU THR PRO CYS GLY ASP VAL GLY LEU VAL SER ALA TYR SEQRES 8 A 161 LEU GLN ALA LEU THR ASN GLU GLY VAL ALA SER VAL LEU SEQRES 9 A 161 VAL ILE SER HIS LEU PRO LEU VAL GLY TYR LEU VAL ALA SEQRES 10 A 161 GLU LEU CYS PRO GLY GLU THR PRO PRO MET PHE THR THR SEQRES 11 A 161 SER ALA ILE ALA SER VAL THR LEU ASP GLU SER GLY ASN SEQRES 12 A 161 GLY THR PHE ASN TRP GLN MET SER PRO CYS ASN LEU LYS SEQRES 13 A 161 MET ALA LYS ALA ILE HET CA A 162 1 HET WO4 A 163 5 HETNAM CA CALCIUM ION HETNAM WO4 TUNGSTATE(VI)ION FORMUL 2 CA CA 2+ FORMUL 3 WO4 O4 W 2- FORMUL 4 HOH *234(H2 O) HELIX 1 1 SER A 17 ARG A 21 5 5 HELIX 2 2 THR A 24 GLN A 41 1 18 HELIX 3 3 PHE A 53 LEU A 67 1 15 HELIX 4 4 PRO A 77 THR A 80 5 4 HELIX 5 5 ASP A 84 GLY A 99 1 16 HELIX 6 6 PRO A 110 CYS A 120 1 11 HELIX 7 7 SER A 151 LEU A 155 5 5 SHEET 1 A 6 GLU A 74 VAL A 75 0 SHEET 2 A 6 ARG A 47 VAL A 50 1 N VAL A 50 O GLU A 74 SHEET 3 A 6 SER A 102 SER A 107 1 O LEU A 104 N LEU A 49 SHEET 4 A 6 GLN A 2 ARG A 7 1 N MET A 6 O VAL A 105 SHEET 5 A 6 ILE A 133 LEU A 138 -1 O VAL A 136 N VAL A 3 SHEET 6 A 6 GLY A 144 MET A 150 -1 O MET A 150 N ILE A 133 LINK NE2 HIS A 8 W WO4 A 163 1555 1555 2.48 LINK O ASP A 65 CA CA A 162 1555 1555 2.61 LINK O GLY A 99 CA CA A 162 3545 1555 2.67 LINK CA CA A 162 O HOH A 297 1555 1555 2.77 LINK CA CA A 162 O HOH A 401 1555 1555 2.84 LINK CA CA A 162 O HOH A 402 1555 1555 2.82 LINK CA CA A 162 O HOH A 403 1555 1555 2.80 LINK CA CA A 162 O HOH A 404 1555 1555 2.80 CISPEP 1 LEU A 109 PRO A 110 0 -0.03 SITE 1 AC1 7 ASP A 65 GLY A 99 HOH A 297 HOH A 401 SITE 2 AC1 7 HOH A 402 HOH A 403 HOH A 404 SITE 1 AC2 7 ARG A 7 HIS A 8 ARG A 55 HIS A 108 SITE 2 AC2 7 LEU A 109 HOH A 273 HOH A 288 CRYST1 39.126 47.737 81.963 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 0.025558 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012201 0.00000