+Open data
-Basic information
Entry | Database: PDB / ID: 1e1d | ||||||
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Title | Hybrid Cluster Protein from Desulfovibrio vulgaris | ||||||
Components | HYDROXYLAMINE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / HYBRID CLUSTER / CUBANE / IRON SULFUR / PRISMANE / FUSCOREDOXIN | ||||||
Function / homology | Function and homology information hydroxylamine reductase / hydroxylamine reductase activity / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO VULGARIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.72 Å | ||||||
Authors | Arendsen, A.F. / Cooper, S.J. / Bailey, S. / Garner, C.D. / Hagen, W.R. / Lindley, P.F. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Hybrid-Cluster Protein (Hcp) from Desulfovibrio Vulgaris (Hildenborough) at 1.6 A Resolution. Authors: Cooper, S.J. / Garner, C.D. / Hagen, W.R. / Lindley, P.F. / Bailey, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e1d.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e1d.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 1e1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e1d_validation.pdf.gz | 968.8 KB | Display | wwPDB validaton report |
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Full document | 1e1d_full_validation.pdf.gz | 971.3 KB | Display | |
Data in XML | 1e1d_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 1e1d_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e1d ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e1d | HTTPS FTP |
-Related 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: 60228.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH NCIMB8303 / Plasmid: PJSP104 / Production host: DESULFOVIBRIO VULGARIS (bacteria) / Strain (production host): HILDENBOROUGH NCIMB8303 / References: UniProt: P31101 |
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#2: Chemical | ChemComp-FSO / |
#3: Chemical | ChemComp-SF4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.9 Details: PROTEIN WAS CRYSTALLISED FROM 0.1M MES PH5.9,60MM MAGNESIUM ACETATE AND 25-30% PEG 8000, pH 5.90 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion / Details: Arendsen, A., (1996) Acta Crystallogr. D.52, 1211. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→21.88 Å / Num. obs: 70418 / % possible obs: 97.2 % / Redundancy: 2.8 % / Rsym value: 0.036 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.72→1.77 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.162 / % possible all: 81.3 |
Reflection | *PLUS Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 81.3 % / Rmerge(I) obs: 0.162 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.72→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: FS4 AND FSO CLUSTER ATOMS REFINED ANISOTROPICALLY
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Displacement parameters | Biso mean: 22.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→12 Å
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Refine LS restraints |
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Software | *PLUS Name: RESTRAIN / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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