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Yorodumi- PDB-3mmj: Structure of the PTP-like phytase from Selenomonas ruminantium in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mmj | ||||||
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Title | Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol hexakisphosphate | ||||||
Components | Myo-inositol hexaphosphate phosphohydrolase | ||||||
Keywords | HYDROLASE / phytase / protein tyrosine phosphatase / inositol phosphate / inositol phosphatase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Selenomonas ruminantium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases. Authors: Gruninger, R.J. / Dobing, S. / Smith, A.D. / Bruder, L.M. / Selinger, L.B. / Wieden, H.J. / Mosimann, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mmj.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mmj.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/3mmj ftp://data.pdbj.org/pub/pdb/validation_reports/mm/3mmj | HTTPS FTP |
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-Related structure data
Related structure data | 3mozC 2b4uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36171.738 Da / Num. of mol.: 2 / Mutation: C252S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Strain: JY35 / Gene: phyA / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WUJ1 |
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-Non-polymers , 6 types, 899 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 8-10% PEG8000, 200-300 NaCl, 50 mM Sodium Acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008 / Details: Double Crystal Si(111) |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→51 Å / Num. all: 120565 / Num. obs: 120565 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 1.5 / Num. unique all: 14414 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B4U Resolution: 1.6→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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