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Yorodumi- PDB-1u26: Crystal structure of Selenomonas ruminantium phytase complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u26 | ||||||
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Title | Crystal structure of Selenomonas ruminantium phytase complexed with persulfated phytate | ||||||
Components | myo-inositol hexaphosphate phosphohydrolase | ||||||
Keywords | HYDROLASE / PTP / P-loop / phytase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Selenomonas ruminantium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chu, H.M. / Guo, R.T. / Lin, T.W. / Chou, C.C. / Shr, H.L. / Lai, H.L. / Tang, T.Y. / Cheng, K.J. / Selinger, B.L. / Wang, A.H.-J. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Structures of Selenomonas ruminantium Phytase in Complex with Persulfated Phytate; DSP Phytase Fold and Mechanism for Sequential Substrate Hydrolysis Authors: Chu, H.M. / Guo, R.T. / Lin, T.W. / Chou, C.C. / Shr, H.L. / Lai, H.L. / Tang, T.Y. / Cheng, K.J. / Selinger, B.L. / Wang, A.H.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u26.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u26.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 1u26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u26 ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u26 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38585.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7WUJ1, EC: 3.1.3.72 #2: Chemical | #3: 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: 2.558 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-HCl, 20mM Ca(OAc)2, 10% PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.071 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.071 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 50763 / Num. obs: 44488 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.299 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.02
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