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Yorodumi- PDB-4oi6: Crystal structure analysis of nickel-bound form SCO4226 from Stre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oi6 | ||||||
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Title | Crystal structure analysis of nickel-bound form SCO4226 from Streptomyces coelicolor A3(2) | ||||||
Components | Nickel responsive protein | ||||||
Keywords | METAL BINDING PROTEIN / nickel responsive protein / Structural Genomics / ferredoxin-like fold / a nickel responsive protein / nickel binding | ||||||
Function / homology | Function and homology information ORF SCO4226, nickel-binding ferredoxin-like monomer / SCO4226-like / SCO4226, nickel-binding ferredoxin-like monomer / Nickel responsive protein SCO4226-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Lu, M. / Jiang, Y.L. / Wang, S. / Cheng, W. / Zhang, R.G. / Virolle, M.J. / Chen, Y. / Zhou, C.Z. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Streptomyces coelicolor SCO4226 Is a Nickel Binding Protein. Authors: Lu, M. / Jiang, Y.L. / Wang, S. / Jin, H. / Zhang, R.G. / Virolle, M.J. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oi6.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oi6.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 4oi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oi6 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oi6 | 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: 10211.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: pET22b / Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO4226 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (de3) / References: UniProt: Q9FCE4 #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-CIT / | #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: 1.63 Å3/Da / Density % sol: 24.44 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.8 M sodium citrate dihydrate, pH 6.5 and 0.8 M NiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→17.536 Å / Num. all: 8509 / Num. obs: 8364 / % possible obs: 98.3 % / Observed criterion σ(F): 1.38 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.04→2.14 Å / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→17.536 Å / SU ML: 0.23 / σ(F): 1.38 / Phase error: 23.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→17.536 Å
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Refine LS restraints |
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LS refinement shell |
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