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Yorodumi- PDB-1qlg: Crystal structure of phytase with magnesium from Bacillus amyloli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qlg | ||||||
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Title | Crystal structure of phytase with magnesium from Bacillus amyloliquefaciens | ||||||
Components | 3-PHYTASE | ||||||
Keywords | PHOSPHOMONOESTERASE / PHYTASE / THERMOSTABLE / PHOSPHATASE / CALCIUM / MAGNESIUM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS AMYLOLIQUEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / DIRECT METHODS / Resolution: 2.2 Å | ||||||
Authors | Shin, S. / Ha, N.-C. / Oh, B.-H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal Structures of a Novel, Thermostable Phytase in Partially and Fully Calcium-Loaded States Authors: Ha, N.-C. / Oh, B.-C. / Shin, S. / Kim, H.J. / Oh, T.K. / Kim, Y.O. / Choi, K.Y. / Oh, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qlg.cif.gz | 84.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qlg.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1qlg ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1qlg | HTTPS FTP |
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-Related structure data
Related structure data | 1cvmC 1pooSC 2pooC 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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Details | BIOLOGICAL_UNIT: MONOMER |
-Components
#1: Protein | Mass: 39007.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CALCIUM MAGNESIUM / Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Strain: DS11 / Cellular location: SECRETION / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: O66037, 3-phytase | ||||
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#2: Chemical | #3: Chemical | #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: 2.21 Å3/Da / Density % sol: 44.47 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and precipitant solutions | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Details: MONOCHROMETER |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 17305 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 1.07 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.62 / Rsym value: 0.317 / % possible all: 87.2 |
Reflection shell | *PLUS % possible obs: 87.2 % |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS Starting model: 1POO Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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