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Yorodumi- PDB-1dkp: CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dkp | ||||||
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Title | CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE AT PH 6.6. PHYTATE IS BOUND WITH ITS 3-PHOSPHATE IN THE ACTIVE SITE. HG2+ CATION ACTS AS AN INTERMOLECULAR BRIDGE | ||||||
Components | PHYTASE | ||||||
Keywords | HYDROLASE / HISTIDINE ACID PHOSPHATASE FOLD | ||||||
Function / homology | Function and homology information 4-phytase activity / inositol phosphate 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.28 Å | ||||||
Authors | Lim, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dkp.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dkp.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dkp_validation.pdf.gz | 886.2 KB | Display | wwPDB validaton report |
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Full document | 1dkp_full_validation.pdf.gz | 893.3 KB | Display | |
Data in XML | 1dkp_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 1dkp_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dkp ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dkp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the single molecule in the asymmetric unit. |
-Components
#1: Protein | Mass: 44696.609 Da / Num. of mol.: 1 / Mutation: A116T, H17A 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 | ||||
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#2: Chemical | ChemComp-HG / #3: Chemical | ChemComp-IHP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: ETHYLENE GLYCOL, GLYCEROL, 2-MORPHOLINOPROPANESULFONIC ACID, MERCURIC CHLORIDE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→25 Å / Num. all: 94671 / Num. obs: 41377 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 22.38 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.088 / % possible all: 89.6 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. all: 48024 / Num. obs: 30534 / % possible obs: 93.7 % / Rmerge(I) obs: 0.039 |
-Processing
Software |
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Refinement | Resolution: 2.28→25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1443774.67 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.44 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.42 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Highest resolution: 2.5 Å / Lowest resolution: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.281 / % reflection Rfree: 4.3 % / Rfactor Rwork: 0.22 |