PDB Short entry for 1UJB HEADER HYDROLASE 31-JUL-03 1UJB TITLE STRUCTURE OF THE PROTEIN HISTIDINE PHOSPHATASE SIXA 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 1UJB 1 REMARK LINK REVDAT 2 24-FEB-09 1UJB 1 VERSN REVDAT 1 25-JAN-05 1UJB 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. 2.06 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 6161139.200 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 9928 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) : 0.173 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1030 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 45.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 748 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE : 0.2080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 80 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 : 1165 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : -0.89000 REMARK 3 B33 (A**2) : 1.03000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.180 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) : 1.500 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.350 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 10.780; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.430 ; 2.500 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 1UJB 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_1000005887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 288 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 IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9936 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 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 (%) : 95.5 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) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 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: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, CACL2, MES, PH 6.6, VAPOR REMARK 280 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 19.63000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.59000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.31000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.59000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.63000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.31000 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 -156.73 -140.37 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 CA A 162 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 65 O REMARK 620 2 GLY A 99 O 146.8 REMARK 620 3 HOH A 187 O 137.9 72.8 REMARK 620 4 HOH A 218 O 84.8 89.5 81.5 REMARK 620 5 HOH A 219 O 90.6 92.1 104.6 173.9 REMARK 620 N 1 2 3 4 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UJC RELATED DB: PDB REMARK 900 1UJC CONTAINS THE SAME PROTEIN COMPLEXED WITH TUNGSTATE. DBREF 1UJB 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 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *113(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 ASP A 65 1 13 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 LYS A 156 1 6 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 TRP A 148 N SER A 135 LINK O ASP A 65 CA CA A 162 1555 1555 2.43 LINK O GLY A 99 CA CA A 162 3545 1555 2.51 LINK CA CA A 162 O HOH A 187 1555 3545 2.87 LINK CA CA A 162 O HOH A 218 1555 1555 2.50 LINK CA CA A 162 O HOH A 219 1555 1555 2.57 CISPEP 1 LEU A 109 PRO A 110 0 0.18 SITE 1 AC1 5 ASP A 65 GLY A 99 HOH A 187 HOH A 218 SITE 2 AC1 5 HOH A 219 CRYST1 39.260 48.620 83.180 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 0.025471 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012022 0.00000