10 20 30 40 50 60 70 80 1DKP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 08-DEC-99 1DKP
TITLE CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI TITLE 2 PHYTASE AT PH 6.6. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE TITLE 3 IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR TITLE 4 BRIDGE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PH 2.5 ACID PHOSPHATASE; COMPND 5 EC: 3.1.3.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET21A
KEYWDS HISTIDINE ACID PHOSPHATASE FOLD, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.LIM,S.GOLOVAN,C.W.FORSBERG,Z.JIA
REVDAT 2 24-FEB-09 1DKP 1 VERSN REVDAT 1 03-AUG-00 1DKP 0
JRNL AUTH D.LIM,S.GOLOVAN,C.W.FORSBERG,Z.JIA JRNL TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI PHYTASE AND JRNL TITL 2 ITS COMPLEX WITH PHYTATE. JRNL REF NAT.STRUCT.BIOL. V. 7 108 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10655611 JRNL DOI 10.1038/72371
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.JIA,S.GOLOVAN,Q.YE,C.W.FORSBERG REMARK 1 TITL PURIFICATION, CRYSTALLIZATION AND PRELIMINARY REMARK 1 TITL 2 X-RAY ANALYSIS OF THE ESCHERICHIA COLI PHYTASE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 54 647 1998 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444997016156 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.DASSA,C.MARCK,P.L.BOQUET REMARK 1 TITL THE COMPLETE NUCLEOTIDE SEQUENCE OF THE REMARK 1 TITL 2 ESCHERICHIA COLI GENE APPA REVEALS SIGNIFICANT REMARK 1 TITL 3 HOMOLOGY BETWEEN PH 2.5 ACID PHOSPHATASE AND REMARK 1 TITL 4 GLUCOSE-1-PHOSPHATASE REMARK 1 REF J.BACTERIOL. V. 172 5497 1990 REMARK 1 REFN ISSN 0021-9193
REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1443774.670 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 41317 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) : 0.189 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2052 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6363 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 288 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3140 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 272 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.41000 REMARK 3 B22 (A**2) : -6.26000 REMARK 3 B33 (A**2) : 2.84000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.82 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) : 1.970 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.780 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.310 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 41.44 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.PA REMARK 3 PARAMETER FILE 2 : WATER_REP.PARA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : PHYTATE.TO REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD
REMARK 4 REMARK 4 1DKP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-99. REMARK 100 THE RCSB ID CODE IS RCSB010165.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-99 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 RU200 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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41377 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.08800 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: NULL REMARK 200 SOFTWARE USED: XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ETHYLENE GLYCOL, GLYCEROL, 2- REMARK 280 MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, PH 6.6, REMARK 280 VAPOR DIFFUSION, HANGING 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 35.28650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.19650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.56350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.19650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.28650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.56350 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE SINGLE MOLECULE IN THE REMARK 300 ASYMMETRIC UNIT.
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 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 ASP A 107 19.15 50.76 REMARK 500 ASN A 126 87.86 179.16 REMARK 500 GLN A 285 130.15 -175.09 REMARK 500 GLN A 287 -146.70 -116.10 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 711 DISTANCE = 5.55 ANGSTROMS
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 HG A 500 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 613 O REMARK 620 2 TYR A 289 O 109.2 REMARK 620 3 HIS A 113 ND1 110.8 79.5 REMARK 620 4 HOH A 820 O 160.8 86.0 82.9 REMARK 620 5 HIS A 158 NE2 79.9 77.8 157.1 92.4 REMARK 620 6 ASP A 154 OD1 71.7 178.3 101.6 92.8 101.0 REMARK 620 7 ASP A 154 OD2 114.9 135.8 81.9 52.0 112.8 43.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 501 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 287 OE1 REMARK 620 2 HOH A 865 O 79.7 REMARK 620 3 HIS A 282 NE2 125.5 78.2 REMARK 620 4 GLN A 285 OE1 107.3 51.0 95.9 REMARK 620 5 LEU A 293 O 116.4 162.6 95.9 114.3 REMARK 620 6 HOH A 866 O 66.2 130.1 151.5 105.1 58.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 502 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HG A 503 HG REMARK 620 2 ASP A 325 OD2 83.2 REMARK 620 3 ASP A 304 OD1 84.3 157.5 REMARK 620 4 IHP A 550 O24 124.8 151.0 47.7 REMARK 620 5 ARG A 16 NH1 110.5 75.1 91.9 98.3 REMARK 620 6 GLU A 219 OE1 157.0 74.2 115.5 78.1 60.1 REMARK 620 7 GLU A 219 OE2 128.1 59.9 141.0 93.3 94.7 41.0 REMARK 620 8 HIS A 250 NE2 75.1 96.9 97.9 85.1 169.2 111.1 74.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 503 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 327 OG1 REMARK 620 2 ASP A 325 OD1 80.5 REMARK 620 3 ASP A 325 OD2 113.1 42.9 REMARK 620 4 THR A 327 O 61.4 76.0 71.0 REMARK 620 5 HIS A 250 NE2 136.4 93.5 88.3 158.3 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 HG A 500 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 501 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 502 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 503 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IHP A 550
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DKL RELATED DB: PDB REMARK 900 PHYTASE AT PH 4.5 (NO LIGAND BOUND) REMARK 900 RELATED ID: 1DKM RELATED DB: PDB REMARK 900 PHYTASE AT PH 6.6 (HG2+ ACTING AS AN INTERMOLECULAR BRIDGE) REMARK 900 RELATED ID: 1DKN RELATED DB: PDB REMARK 900 PHYTASE AT PH 5.0 (HG2+ ACTING AS AN INTERMOLECULAR BRIDGE) REMARK 900 RELATED ID: 1DKO RELATED DB: PDB REMARK 900 PHYTASE AT PH 6.6 (TUNGSTATE BOUND AT THE ACTIVE SITE, HG2+ REMARK 900 ACTING AS AN INTERMOLECULAR BRIDGE) REMARK 900 RELATED ID: 1DKQ RELATED DB: PDB REMARK 900 PHYTASE AT PH 5.0 (PHYTATE BOUND IN ACTIVE SITE, HG2+ REMARK 900 ACTING AS AN INTERMOLECULAR BRIDGE)
DBREF 1DKP A 1 410 UNP P07102 PPA_ECOLI 23 432
SEQADV 1DKP ALA A 17 UNP P07102 HIS 39 ENGINEERED SEQADV 1DKP THR A 116 UNP P07102 ALA 138 ENGINEERED
SEQRES 1 A 410 GLN SER GLU PRO GLU LEU LYS LEU GLU SER VAL VAL ILE SEQRES 2 A 410 VAL SER ARG ALA GLY VAL ARG ALA PRO THR LYS ALA THR SEQRES 3 A 410 GLN LEU MET GLN ASP VAL THR PRO ASP ALA TRP PRO THR SEQRES 4 A 410 TRP PRO VAL LYS LEU GLY TRP LEU THR PRO ARG GLY GLY SEQRES 5 A 410 GLU LEU ILE ALA TYR LEU GLY HIS TYR GLN ARG GLN ARG SEQRES 6 A 410 LEU VAL ALA ASP GLY LEU LEU ALA LYS LYS GLY CYS PRO SEQRES 7 A 410 GLN SER GLY GLN VAL ALA ILE ILE ALA ASP VAL ASP GLU SEQRES 8 A 410 ARG THR ARG LYS THR GLY GLU ALA PHE ALA ALA GLY LEU SEQRES 9 A 410 ALA PRO ASP CYS ALA ILE THR VAL HIS THR GLN THR ASP SEQRES 10 A 410 THR SER SER PRO ASP PRO LEU PHE ASN PRO LEU LYS THR SEQRES 11 A 410 GLY VAL CYS GLN LEU ASP ASN ALA ASN VAL THR ASP ALA SEQRES 12 A 410 ILE LEU SER ARG ALA GLY GLY SER ILE ALA ASP PHE THR SEQRES 13 A 410 GLY HIS ARG GLN THR ALA PHE ARG GLU LEU GLU ARG VAL SEQRES 14 A 410 LEU ASN PHE PRO GLN SER ASN LEU CYS LEU LYS ARG GLU SEQRES 15 A 410 LYS GLN ASP GLU SER CYS SER LEU THR GLN ALA LEU PRO SEQRES 16 A 410 SER GLU LEU LYS VAL SER ALA ASP ASN VAL SER LEU THR SEQRES 17 A 410 GLY ALA VAL SER LEU ALA SER MET LEU THR GLU ILE PHE SEQRES 18 A 410 LEU LEU GLN GLN ALA GLN GLY MET PRO GLU PRO GLY TRP SEQRES 19 A 410 GLY ARG ILE THR ASP SER HIS GLN TRP ASN THR LEU LEU SEQRES 20 A 410 SER LEU HIS ASN ALA GLN PHE TYR LEU LEU GLN ARG THR SEQRES 21 A 410 PRO GLU VAL ALA ARG SER ARG ALA THR PRO LEU LEU ASP SEQRES 22 A 410 LEU ILE LYS THR ALA LEU THR PRO HIS PRO PRO GLN LYS SEQRES 23 A 410 GLN ALA TYR GLY VAL THR LEU PRO THR SER VAL LEU PHE SEQRES 24 A 410 ILE ALA GLY HIS ASP THR ASN LEU ALA ASN LEU GLY GLY SEQRES 25 A 410 ALA LEU GLU LEU ASN TRP THR LEU PRO GLY GLN PRO ASP SEQRES 26 A 410 ASN THR PRO PRO GLY GLY GLU LEU VAL PHE GLU ARG TRP SEQRES 27 A 410 ARG ARG LEU SER ASP ASN SER GLN TRP ILE GLN VAL SER SEQRES 28 A 410 LEU VAL PHE GLN THR LEU GLN GLN MET ARG ASP LYS THR SEQRES 29 A 410 PRO LEU SER LEU ASN THR PRO PRO GLY GLU VAL LYS LEU SEQRES 30 A 410 THR LEU ALA GLY CYS GLU GLU ARG ASN ALA GLN GLY MET SEQRES 31 A 410 CYS SER LEU ALA GLY PHE THR GLN ILE VAL ASN GLU ALA SEQRES 32 A 410 ARG ILE PRO ALA CYS SER LEU
HET HG A 500 1 HET HG A 501 1 HET HG A 502 1 HET HG A 503 1 HET IHP A 550 36
HETNAM HG MERCURY (II) ION HETNAM IHP INOSITOL HEXAKISPHOSPHATE
HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE
FORMUL 2 HG 4(HG 2+) FORMUL 6 IHP C6 H18 O24 P6 FORMUL 7 HOH *272(H2 O)
HELIX 1 1 THR A 26 VAL A 32 1 7 HELIX 2 2 THR A 48 ASP A 69 1 22 HELIX 3 3 ASP A 90 ALA A 105 1 16 HELIX 4 4 ASP A 122 ASN A 126 5 5 HELIX 5 5 ASP A 136 ALA A 148 1 13 HELIX 6 6 SER A 151 HIS A 158 1 8 HELIX 7 7 ARG A 159 ASN A 171 1 13 HELIX 8 8 PHE A 172 GLN A 174 5 3 HELIX 9 9 SER A 175 LYS A 180 1 6 HELIX 10 10 SER A 189 LEU A 194 1 6 HELIX 11 11 GLY A 209 GLY A 228 1 20 HELIX 12 12 GLU A 231 ARG A 236 5 6 HELIX 13 13 ASP A 239 GLN A 258 1 20 HELIX 14 14 THR A 260 THR A 280 1 21 HELIX 15 15 ALA A 288 GLY A 290 5 3 HELIX 16 16 HIS A 303 GLU A 315 1 13 HELIX 17 17 THR A 356 ASP A 362 1 7 HELIX 18 18 LEU A 393 ARG A 404 1 12 HELIX 19 19 ILE A 405 SER A 409 5 5
SHEET 1 A 7 VAL A 112 HIS A 113 0 SHEET 2 A 7 VAL A 83 ALA A 87 1 O ILE A 85 N HIS A 113 SHEET 3 A 7 VAL A 297 GLY A 302 1 O VAL A 297 N ALA A 84 SHEET 4 A 7 LEU A 6 ARG A 16 1 O VAL A 11 N LEU A 298 SHEET 5 A 7 GLU A 332 ARG A 340 -1 N LEU A 333 O VAL A 14 SHEET 6 A 7 GLN A 346 PHE A 354 -1 O TRP A 347 N TRP A 338 SHEET 7 A 7 GLY A 373 LEU A 377 -1 O GLY A 373 N PHE A 354 SHEET 1 A1 7 VAL A 112 HIS A 113 0 SHEET 2 A1 7 VAL A 83 ALA A 87 1 O ILE A 85 N HIS A 113 SHEET 3 A1 7 VAL A 297 GLY A 302 1 O VAL A 297 N ALA A 84 SHEET 4 A1 7 LEU A 6 ARG A 16 1 O VAL A 11 N LEU A 298 SHEET 5 A1 7 GLU A 332 ARG A 340 -1 N LEU A 333 O VAL A 14 SHEET 6 A1 7 GLN A 346 PHE A 354 -1 O TRP A 347 N TRP A 338 SHEET 7 A1 7 CYS A 391 SER A 392 -1 O CYS A 391 N ILE A 348 SHEET 1 B 2 LEU A 198 VAL A 200 0 SHEET 2 B 2 VAL A 205 LEU A 207 -1 O SER A 206 N LYS A 199 SHEET 1 C 2 GLN A 285 LYS A 286 0 SHEET 2 C 2 THR A 292 LEU A 293 -1 N LEU A 293 O GLN A 285
SSBOND 1 CYS A 77 CYS A 108 1555 1555 2.03 SSBOND 2 CYS A 133 CYS A 408 1555 1555 2.03 SSBOND 3 CYS A 178 CYS A 188 1555 1555 2.03 SSBOND 4 CYS A 382 CYS A 391 1555 1555 2.03
LINK HG HG A 500 O HOH A 613 1555 1555 2.83 LINK HG HG A 500 O TYR A 289 1555 1555 2.88 LINK HG HG A 500 ND1 HIS A 113 1555 1555 2.59 LINK HG HG A 500 O HOH A 820 1555 1555 3.07 LINK HG HG A 501 OE1 GLN A 287 1555 1555 3.07 LINK HG HG A 501 O HOH A 865 1555 1555 2.85 LINK HG HG A 501 NE2 HIS A 282 1555 1555 2.62 LINK HG HG A 501 OE1 GLN A 285 1555 1555 3.14 LINK HG HG A 501 O LEU A 293 1555 1555 2.74 LINK HG HG A 501 O HOH A 866 1555 1555 2.79 LINK HG HG A 502 HG HG A 503 1555 1555 1.67 LINK HG HG A 502 OD2 ASP A 325 1555 1555 2.76 LINK HG HG A 502 OD1 ASP A 304 1555 1555 3.02 LINK HG HG A 502 O24 IHP A 550 1555 1555 3.19 LINK HG HG A 502 NH1 ARG A 16 1555 1555 2.85 LINK HG HG A 502 OE1 GLU A 219 1555 1555 3.26 LINK HG HG A 502 OE2 GLU A 219 1555 1555 2.99 LINK HG HG A 502 NE2 HIS A 250 1555 1555 2.63 LINK HG HG A 503 OG1 THR A 327 1555 1555 2.59 LINK HG HG A 503 OD1 ASP A 325 1555 1555 2.89 LINK HG HG A 503 OD2 ASP A 325 1555 1555 3.05 LINK HG HG A 503 O THR A 327 1555 1555 2.99 LINK HG HG A 503 NE2 HIS A 250 1555 1555 2.73 LINK HG HG A 500 NE2 HIS A 158 1555 3555 2.47 LINK HG HG A 500 OD1 ASP A 154 1555 3555 2.80 LINK HG HG A 500 OD2 ASP A 154 1555 3555 3.06
CISPEP 1 LEU A 293 PRO A 294 0 -0.03
SITE 1 AC1 6 HIS A 113 ASP A 154 HIS A 158 TYR A 289 SITE 2 AC1 6 HOH A 613 HOH A 820 SITE 1 AC2 6 HIS A 282 GLN A 285 GLN A 287 LEU A 293 SITE 2 AC2 6 HOH A 865 HOH A 866 SITE 1 AC3 8 ARG A 16 GLU A 219 HIS A 250 ASP A 304 SITE 2 AC3 8 ASP A 325 THR A 327 HG A 503 IHP A 550 SITE 1 AC4 5 HIS A 250 ASP A 304 ASP A 325 THR A 327 SITE 2 AC4 5 HG A 502 SITE 1 AC5 20 ARG A 16 ARG A 20 THR A 23 LYS A 24 SITE 2 AC5 20 ASP A 90 ARG A 92 MET A 216 HIS A 250 SITE 3 AC5 20 PHE A 254 ARG A 267 HIS A 303 ASP A 304 SITE 4 AC5 20 THR A 305 HG A 502 HOH A 635 HOH A 644 SITE 5 AC5 20 HOH A 655 HOH A 727 HOH A 752 HOH A 821
CRYST1 70.573 75.127 90.393 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 0.014170 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013311 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011063 0.00000