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- PDB-1dkl: CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAN... -

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Basic information

Entry
Database: PDB / ID: 1dkl
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 4.5 (NO LIGAND BOUND)
ComponentsPHYTASE
KeywordsHYDROLASE / HISTIDINE ACID PHOSPHATASE FOLD
Function / homology
Function and homology information


inositol phosphate phosphatase activity / inositol hexakisphosphate 4-phosphatase activity / cellular response to anoxia / nucleotidase activity / sugar-phosphatase activity / acid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / cellular response to phosphate starvation / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / outer membrane-bounded periplasmic space / GTPase activity
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsLim, D. / Golovan, S. / Forsberg, C.W. / Jia, Z.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structures of Escherichia coli phytase and its complex with phytate.
Authors: Lim, D. / Golovan, S. / Forsberg, C.W. / Jia, Z.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Purification, Crystallization and Preliminary X-ray Analysis of the Escherichia coli Phytase
Authors: Jia, Z. / Golovan, S. / Ye, Q. / Forsberg, C.W.
#2: Journal: J.Bacteriol. / Year: 1990
Title: The Complete Nucleotide Sequence of the Escherichia coli Gene appA Reveals Significant Homology Between pH 2.5 Acid Phosphatase and Glucose-1-phosphatase
Authors: Dassa, J. / Marck, C. / Boquet, P.L.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHYTASE
B: PHYTASE


Theoretical massNumber of molelcules
Total (without water)89,4672
Polymers89,4672
Non-polymers00
Water6,179343
1
A: PHYTASE


Theoretical massNumber of molelcules
Total (without water)44,7341
Polymers44,7341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHYTASE


Theoretical massNumber of molelcules
Total (without water)44,7341
Polymers44,7341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.802, 72.126, 82.434
Angle α, β, γ (deg.)90.00, 92.04, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer of the dimer in the asymmetric unit.

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Components

#1: Protein PHYTASE / PH 2.5 ACID PHOSPHATASE


Mass: 44733.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: P07102, acid phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 273 K / Method: small tubes / pH: 4.5
Details: SODIUM ACETATE, pH 4.5, SMALL TUBES, temperature 273K
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
172 mg/mlprotein1drop
22.5 mM1dropHgCl2
328 %ethylene glycol1reservoir
418 %glycerol1reservoir
533 mMMops1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 21, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 106657 / Num. obs: 37076 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.46
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.231 / % possible all: 97
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.3→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1606397.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3710 10 %RANDOM
Rwork0.157 ---
all0.157 37040 --
obs0.157 37040 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.82 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å2-2.92 Å2
2---1.22 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6167 0 0 343 6510
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.511.5
X-RAY DIFFRACTIONc_mcangle_it3.462
X-RAY DIFFRACTIONc_scbond_it4.542
X-RAY DIFFRACTIONc_scangle_it5.882.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 670 10.9 %
Rwork0.19 5505 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER_REP.TOP

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