+Open data
-Basic information
Entry | Database: PDB / ID: 2bgm | ||||||
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Title | X-Ray structure of ternary-Secoisolariciresinol Dehydrogenase | ||||||
Components | RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE | ||||||
Keywords | XIDOREDUCTASE / OXIDOREDUCTASE / DEHYDROGENASE | ||||||
Function / homology | Function and homology information secoisolariciresinol dehydrogenase / (-)-secoisolariciresinol dehydrogenase activity / lignan biosynthetic process / protein homotetramerization / nucleotide binding Similarity search - Function | ||||||
Biological species | PODOPHYLLUM PELTATUM (plant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Youn, B. / Moinuddin, S.G. / Davin, L.B. / Lewis, N.G. / Kang, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal Structures of Apo-Form and Binary/Ternary Complexes of Podophyllum Secoisolariciresinol Dehydrogenase, an Enzyme Involved in Formation of Health-Protecting and Plant Defense Lignans Authors: Youn, B. / Moinuddin, S.G. / Davin, L.B. / Lewis, N.G. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bgm.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bgm.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 2bgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bgm_validation.pdf.gz | 534.9 KB | Display | wwPDB validaton report |
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Full document | 2bgm_full_validation.pdf.gz | 549.6 KB | Display | |
Data in XML | 2bgm_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2bgm_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/2bgm ftp://data.pdbj.org/pub/pdb/validation_reports/bg/2bgm | HTTPS FTP |
-Related structure data
Related structure data | 2bgkC 2bglC 1bgkS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29285.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PODOPHYLLUM PELTATUM (plant) / Plasmid: PTRCHIS2-TOPO TA VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: Q94KL8 |
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#2: Chemical | ChemComp-NAJ / |
#3: Chemical | ChemComp-MAX / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.52 % |
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Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU STURN 92 / Wavelength: 1.54 |
Detector | Type: RIGAKU CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 12187 / % possible obs: 79.1 % / Observed criterion σ(I): 2 / Redundancy: 5.81 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.2 / % possible all: 13.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BGK Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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