10 20 30 40 50 60 70 80 1DKN - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 08-DEC-99 1DKN
TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 5.0 TITLE 2 WITH HG2+ CATION ACTING AS AN INTERMOLECULAR 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 1DKN 1 VERSN REVDAT 1 03-AUG-00 1DKN 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1353378.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 33634 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) : 0.223 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1681 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5260 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 301 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3145 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.63000 REMARK 3 B22 (A**2) : -11.59000 REMARK 3 B33 (A**2) : 14.22000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80 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) : 1.790 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.750 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.740 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.630 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 51.04 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 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD
REMARK 4 REMARK 4 1DKN 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 RCSB010163.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-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 : 33792 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 92.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.15200 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 (%): 53.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 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 35.22150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.91450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.35050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.91450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.22150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.35050 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 HIS A 17 170.41 -56.33 REMARK 500 ALA A 25 56.95 -156.68 REMARK 500 THR A 26 -179.68 -66.42 REMARK 500 ASP A 107 -8.38 66.49 REMARK 500 ASN A 126 92.81 171.65 REMARK 500 LYS A 183 53.30 -119.81 REMARK 500 GLN A 184 16.75 -64.13 REMARK 500 PRO A 230 -71.67 -31.29 REMARK 500 GLN A 285 134.66 -171.85 REMARK 500 GLN A 287 -153.57 -122.70 REMARK 500 THR A 295 -121.93 -155.83 REMARK 500 SER A 296 -52.09 -134.85 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 630 DISTANCE = 5.07 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 HIS A 113 ND1 REMARK 620 2 HOH A 708 O 104.9 REMARK 620 3 HOH A 723 O 53.6 78.0 REMARK 620 4 TYR A 289 O 85.3 104.4 136.9 REMARK 620 5 ASP A 154 OD1 112.4 95.5 69.9 149.1 REMARK 620 6 HIS A 158 NE2 158.5 81.8 147.2 73.3 86.7 REMARK 620 7 ASP A 154 OD2 72.8 111.6 44.8 141.4 40.0 124.3 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 HIS A 250 NE2 REMARK 620 2 ASP A 325 OD2 103.6 REMARK 620 3 HOH A 690 O 89.0 84.3 REMARK 620 4 ARG A 16 NH1 174.9 74.3 95.4 REMARK 620 5 ARG A 16 NH2 127.8 115.8 126.3 51.0 REMARK 620 6 GLU A 219 OE1 73.9 124.1 149.3 103.3 56.2 REMARK 620 7 ASP A 304 OD1 94.7 154.0 77.8 88.8 63.4 78.5 REMARK 620 8 HOH A 691 O 102.9 53.1 137.3 72.0 77.6 72.6 140.0 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 502 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 282 NE2 REMARK 620 2 GLN A 285 OE1 93.9 REMARK 620 3 HOH A 715 O 86.5 72.6 REMARK 620 4 GLN A 287 OE1 138.1 76.8 51.6 REMARK 620 5 LEU A 293 O 90.7 105.1 176.3 131.2 REMARK 620 6 GLN A 287 NE2 118.7 113.6 55.7 39.6 128.0 REMARK 620 N 1 2 3 4 5 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 HG A 504 HG REMARK 620 2 THR A 295 N 107.1 REMARK 620 3 ALA A 278 O 89.5 155.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 504 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 11 O REMARK 620 2 SER A 296 O 64.0 REMARK 620 3 SER A 10 OG 96.9 69.4 REMARK 620 N 1 2
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 HG A 504
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: 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: 1DKP RELATED DB: PDB REMARK 900 PHYTASE AT PH 6.6 (PHYTATE BOUND IN 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 1DKN A 1 410 UNP P07102 PPA_ECOLI 23 432
SEQADV 1DKN 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 HIS 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 HG A 504 1
HETNAM HG MERCURY (II) ION
FORMUL 2 HG 5(HG 2+) FORMUL 7 HOH *136(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 ASP A 239 GLN A 258 1 20 HELIX 13 13 THR A 260 THR A 280 1 21 HELIX 14 14 ALA A 288 GLY A 290 5 3 HELIX 15 15 HIS A 303 GLU A 315 1 13 HELIX 16 16 THR A 356 ASP A 362 1 7 HELIX 17 17 LEU A 393 ARG A 404 1 12 HELIX 18 18 ILE A 405 SER A 409 5 5
SHEET 1 A 6 VAL A 83 ALA A 87 0 SHEET 2 A 6 VAL A 297 GLY A 302 1 O VAL A 297 N ALA A 84 SHEET 3 A 6 LEU A 6 ARG A 16 1 O VAL A 11 N LEU A 298 SHEET 4 A 6 GLU A 332 ARG A 340 -1 N LEU A 333 O VAL A 14 SHEET 5 A 6 SER A 345 PHE A 354 -1 O SER A 345 N ARG A 340 SHEET 6 A 6 GLY A 373 LEU A 377 -1 N GLY A 373 O PHE A 354 SHEET 1 A1 6 VAL A 83 ALA A 87 0 SHEET 2 A1 6 VAL A 297 GLY A 302 1 O VAL A 297 N ALA A 84 SHEET 3 A1 6 LEU A 6 ARG A 16 1 O VAL A 11 N LEU A 298 SHEET 4 A1 6 GLU A 332 ARG A 340 -1 N LEU A 333 O VAL A 14 SHEET 5 A1 6 SER A 345 PHE A 354 -1 O SER A 345 N ARG A 340 SHEET 6 A1 6 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 2.04 SSBOND 4 CYS A 382 CYS A 391 1555 1555 2.03
LINK HG HG A 500 ND1 HIS A 113 1555 1555 2.48 LINK HG HG A 501 NE2 HIS A 250 1555 1555 2.49 LINK HG HG A 502 NE2 HIS A 282 1555 1555 2.64 LINK HG HG A 500 O HOH A 708 1555 1555 2.82 LINK HG HG A 500 O HOH A 723 1555 1555 3.28 LINK HG HG A 500 O TYR A 289 1555 1555 2.96 LINK HG HG A 501 OD2 ASP A 325 1555 1555 2.71 LINK HG HG A 501 O HOH A 690 1555 1555 2.77 LINK HG HG A 501 NH1 ARG A 16 1555 1555 2.50 LINK HG HG A 501 NH2 ARG A 16 1555 1555 2.80 LINK HG HG A 501 OE1 GLU A 219 1555 1555 2.90 LINK HG HG A 501 OD1 ASP A 304 1555 1555 3.29 LINK HG HG A 501 O HOH A 691 1555 1555 2.95 LINK HG HG A 502 OE1 GLN A 285 1555 1555 3.20 LINK HG HG A 502 O HOH A 715 1555 1555 2.96 LINK HG HG A 502 OE1 GLN A 287 1555 1555 3.07 LINK HG HG A 502 O LEU A 293 1555 1555 2.60 LINK HG HG A 502 NE2 GLN A 287 1555 1555 3.50 LINK HG HG A 503 HG HG A 504 1555 1555 3.14 LINK HG HG A 503 N THR A 295 1555 1555 2.76 LINK HG HG A 503 O ALA A 278 1555 1555 2.66 LINK HG HG A 504 O VAL A 11 1555 1555 3.13 LINK HG HG A 504 O SER A 296 1555 1555 3.52 LINK HG HG A 504 OG SER A 10 1555 1555 3.17 LINK HG HG A 500 OD1 ASP A 154 1555 3555 2.79 LINK HG HG A 500 NE2 HIS A 158 1555 3555 2.42 LINK HG HG A 500 OD2 ASP A 154 1555 3555 3.40
CISPEP 1 LEU A 293 PRO A 294 0 0.01
SITE 1 AC1 5 HIS A 113 ASP A 154 HIS A 158 TYR A 289 SITE 2 AC1 5 HOH A 708 SITE 1 AC2 7 ARG A 16 GLU A 219 HIS A 250 ASP A 304 SITE 2 AC2 7 ASP A 325 HOH A 690 HOH A 691 SITE 1 AC3 5 HIS A 282 GLN A 285 GLN A 287 LEU A 293 SITE 2 AC3 5 HOH A 715 SITE 1 AC4 4 ALA A 278 PRO A 294 THR A 295 HG A 504 SITE 1 AC5 5 SER A 10 VAL A 11 SER A 296 LEU A 298 SITE 2 AC5 5 HG A 503
CRYST1 70.443 74.701 89.829 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 0.014196 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013387 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011132 0.00000