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Yorodumi- PDB-1h6l: beta-propeller phytase in complex with phosphate and calcium ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h6l | ||||||
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Title | beta-propeller phytase in complex with phosphate and calcium ions | ||||||
Components | 3-PHYTASE | ||||||
Keywords | HYDROLASE / PHOSPHATASE / PHYTASE / PROPELLER / PHOSPHATE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS AMYLOLIQUEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shin, S. / Ha, N.C. / Oh, B.H. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Enzyme Mechanism and Catalytic Property of Beta Propeller Phytase Authors: Shin, S. / Ha, N.C. / Oh, B.H. / Oh, T. / 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 | 1h6l.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h6l.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1h6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h6l_validation.pdf.gz | 371.6 KB | Display | wwPDB validaton report |
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Full document | 1h6l_full_validation.pdf.gz | 372.2 KB | Display | |
Data in XML | 1h6l_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1h6l_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6l ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6l | HTTPS FTP |
-Related structure data
Related structure data | 2pooS S: Starting model for refinement |
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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
#1: Protein | Mass: 38821.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Strain: DS11 / References: UniProt: O66037, 3-phytase | ||||
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#2: Chemical | ChemComp-CA / #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: 2.23 Å3/Da / Density % sol: 44.87 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Ha, N.C., (1999) Acta Crystallogr, D55, 691. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 32362 / % possible obs: 94.7 % / Observed criterion σ(I): 1 / Redundancy: 7.73 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3 / % possible all: 80.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 250463 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2POO Resolution: 1.8→20 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |