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Yorodumi- PDB-1dkm: CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH HG2+... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dkm | ||||||
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Title | CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHYTASE AT PH 6.6 WITH HG2+ CATION ACTING AS AN INTERMOLECULAR BRIDGE | ||||||
Components | PHYTASE | ||||||
Keywords | HYDROLASE / HISTIDINE ACID PHOSPHATASE FOLD | ||||||
Function / homology | Function and homology information inositol phosphate phosphatase activity / 4-phytase activity / cellular response to anoxia / sugar-phosphatase activity / nucleotidase 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 / dephosphorylation ...inositol phosphate phosphatase activity / 4-phytase activity / cellular response to anoxia / sugar-phosphatase activity / nucleotidase 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 / dephosphorylation / outer membrane-bounded periplasmic space / GTPase activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 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 | 1dkm.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dkm.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dkm ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dkm | HTTPS FTP |
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-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: 44763.680 Da / Num. of mol.: 1 / Mutation: A116T 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: 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: 2.64 Å3/Da / Density % sol: 53.42 % | ||||||||||||||||||||||||||||||||||||
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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: Jan 23, 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: 2.25→25 Å / Num. all: 82456 / Num. obs: 82456 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.75 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.085 / % possible all: 98.6 |
Reflection | *PLUS Num. obs: 42339 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Resolution: 2.25→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1477031.73 / 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: 41.96 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.015 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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