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Yorodumi- PDB-1e1k: ADRENODOXIN REDUCTASE in complex with NADP+ obtained by a soaking... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e1k | ||||||
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Title | ADRENODOXIN REDUCTASE in complex with NADP+ obtained by a soaking experiment | ||||||
Components | ADRENODOXIN REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NADP+ / FLAVOENZYME / ELECTRON TRANSFERASE | ||||||
Function / homology | Function and homology information adrenodoxin-NADP+ reductase / NADPH-adrenodoxin reductase activity / ubiquinone biosynthetic process / steroid biosynthetic process / cholesterol metabolic process / electron transport chain / NADP binding / flavin adenine dinucleotide binding / mitochondrial inner membrane / mitochondrion Similarity search - Function | ||||||
Biological species | BOVINE (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ziegler, G.A. / Schulz, G.E. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal Structures of Adrenodoxin Reductase in Complex with Nadp+ and Nadph Suggesting a Mechanism for the Electron Transfer of an Enzyme Family Authors: Ziegler, G.A. / Schulz, G.E. #1: Journal: J.Mol.Biol. / Year: 1999 Title: The Structure of Adrenodoxin Reductase of Mitochondrial P450 Systems: Electron Transfer for Steroid Biosynthesis Authors: Ziegler, G.A. / Vonrhein, C. / Hanukoglu, I. / Schulz, G.E. #2: Journal: FEBS Lett. / Year: 1999 Title: Chaperone-Assisted Expression of Authentic Bovine Adrenodoxin Reductase in Escherichia Coli Authors: Vonrhein, C. / Schmidt, U. / Ziegler, G.A. / Schweiger, S. / Hanukoglu, I. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e1k.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e1k.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 1e1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e1k_validation.pdf.gz | 995 KB | Display | wwPDB validaton report |
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Full document | 1e1k_full_validation.pdf.gz | 1007.2 KB | Display | |
Data in XML | 1e1k_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 1e1k_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e1k ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e1k | HTTPS FTP |
-Related structure data
Related structure data | 1e1lC 1e1mC 1e1nC 1cjcS 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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-Components
#1: Protein | Mass: 50360.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOVINE (cattle) / Tissue: STEROIDOGENIC TISSUES STEROIDOGENIC TISSUES / Cellular location: MITOCHONDRIAL MATRIX / Organelle: MITOCHONDRIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08165 |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
Sequence details | FIRST 32 RESIDUES OF SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS DELETED ...FIRST 32 RESIDUES OF SWISS-PROT SEQUENCE REFER TO A MITOCHONDR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Date: Jul 15, 1999 |
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: 1.95→20 Å / Num. obs: 41174 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.069 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.33 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 26 Å / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.33 |
-Processing
Software | Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CJC Resolution: 1.95→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 26.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 29 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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