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Yorodumi- PDB-1yk4: Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yk4 | ||||||
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Title | Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W4L/R5S | ||||||
Components | Rubredoxin | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.69 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 | 1yk4.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yk4.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/1yk4 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/1yk4 | HTTPS FTP |
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-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: 5772.364 Da / Num. of mol.: 1 / Mutation: W4L, R5S 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 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.936664 Å3/Da / Density % sol: 36.488735 % / Description: the file contains Friedel pairs |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Sodium malonate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.7301 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 4, 2004 |
Radiation | Monochromator: Double crystal focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7301 Å / Relative weight: 1 |
Reflection | Resolution: 0.69→20 Å / Num. obs: 132784 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 3.6 Å2 / Rsym value: 0.039 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 0.69→0.7 Å / Num. unique all: 2695 / Rsym value: 0.22 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.69→20 Å / Num. parameters: 5141 / Num. restraintsaints: 1619 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): -1 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.87 Å2 | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 367.02 / Occupancy sum non hydrogen: 487.02 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.69→20 Å
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Refine LS restraints |
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