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- PDB-1dkp: CRYSTAL STRUCTURE OF PHYTATE COMPLEX OF ESCHERICHIA COLI PHYTASE ... -
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Open data
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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 | ||||||
![]() | PHYTASE | ||||||
![]() | HYDROLASE / HISTIDINE ACID PHOSPHATASE FOLD | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Lim, D. / Golovan, S. / Forsberg, C.W. / Jia, Z. | ||||||
![]() | ![]() Title: Crystal structures of Escherichia coli phytase and its complex with phytate. Authors: Lim, D. / Golovan, S. / Forsberg, C.W. / Jia, Z. #1: ![]() Title: Purification, Crystallization and Preliminary X-ray Analysis of the Escherichia coli Phytase Authors: Jia, Z. / Golovan, S. / Ye, Q. / Forsberg, C.W. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.3 KB | Display | ![]() |
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PDB format | ![]() | 75.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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. |
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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.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HG / #3: Chemical | ChemComp-IHP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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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 |