+Open data
-Basic information
Entry | Database: PDB / ID: 1ayf | ||||||
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Title | BOVINE ADRENODOXIN (OXIDIZED) | ||||||
Components | ADRENODOXIN | ||||||
Keywords | ELECTRON TRANSPORT / [2FE-2S]FERREDOXIN / ADRENODOXIN | ||||||
Function / homology | Function and homology information Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / respiratory electron transport chain / cholesterol metabolic process ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / respiratory electron transport chain / cholesterol metabolic process / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Mueller, A. / Mueller, J.J. / Heinemann, U. | ||||||
Citation | Journal: Structure / Year: 1998 Title: New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108). Authors: Muller, A. / Muller, J.J. / Muller, Y.A. / Uhlmann, H. / Bernhardt, R. / Heinemann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ayf.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ayf.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ayf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ayf_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 1ayf_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 1ayf_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1ayf_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayf ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayf | 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.328, 0.9268, 0.183), Vector: |
-Components
#1: Protein | Mass: 11661.205 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: ADRENAL GLAND / Organelle: MITOCHONDRION / Plasmid: PKKHC, PMIXT / Production host: Escherichia coli (E. coli) / Strain (production host): HB 101 / References: UniProt: P00257 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 4000, 10% GLYCEROL, 100 MM TRIS, PH 7.4, 100MM MGCL2, 20 MG/ML PROTEIN | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→11 Å / Num. obs: 21775 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.044 / Net I/σ(I): 30.956 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 7.74 / Rsym value: 0.204 / % possible all: 99.1 |
Reflection | *PLUS Lowest resolution: 10 Å / Rmerge(I) obs: 0.044 / Biso Wilson estimate: 16.4 Å2 |
Reflection shell | *PLUS Redundancy: 5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 7.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→11 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→11 Å
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Refine LS restraints |
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Software | *PLUS Name: CCP4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |