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Yorodumi- PDB-2p4h: Crystal Structure of Vestitone Reductase from Alfalfa (Medicago s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p4h | ||||||
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Title | Crystal Structure of Vestitone Reductase from Alfalfa (Medicago sativa L.) | ||||||
Components | Vestitone reductase | ||||||
Keywords | PLANT PROTEIN / NADPH-dependent reductase / isoflavonoid | ||||||
Function / homology | Function and homology information (3R)-2'-hydroxyisoflavanone reductase / flavonoid biosynthetic process / defense response / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Wang, X. / Shao, H. / Dixon, R.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of Vestitone Reductase from Alfalfa (Medicago sativa L.). Authors: Shao, H. / Dixon, R.A. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p4h.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4h.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 2p4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p4h_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 2p4h_full_validation.pdf.gz | 430 KB | Display | |
Data in XML | 2p4h_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2p4h_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4h ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4h | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a monomer. |
-Components
#1: Protein | Mass: 35571.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Gene: Vestitone Reductase / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q40316 |
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#2: 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: 2.82 Å3/Da / Density % sol: 56.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 6000, 0.1M magnesium chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789, 0.9791, 0.9641 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2006 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Double Crystal Monochromator Si(111) and Si(220) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→27.6 Å / Num. all: 77901 / Num. obs: 77901 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.051 / Net I/σ(I): 26.6 | ||||||||||||
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 7639 / Rsym value: 0.392 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→27.61 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→27.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008
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