+Open data
-Basic information
Entry | Database: PDB / ID: 1yk5 | ||||||
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Title | Pyrococcus abyssi rubredoxin | ||||||
Components | Rubredoxin | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Bonisch, H. / Schmidt, C.L. / Bianco, P. / Ladenstein, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S. Authors: Bonisch, H. / Schmidt, C.L. / Bianco, P. / Ladenstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yk5.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yk5.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 1yk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/1yk5 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/1yk5 | HTTPS FTP |
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-Related structure data
Related structure data | 1yk4C 1brfS 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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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 6046.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: rub / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9V099 #2: Chemical | ChemComp-FE / #3: 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: 2.77 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: Ammonium sulfate, MES, Dioxane, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2002 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→40.37 Å / Num. obs: 24841 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.78→1.81 Å / Rsym value: 0.504 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BRF Resolution: 1.79→40.37 Å / Isotropic thermal model: Individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→40.37 Å
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Refine LS restraints |
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