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Yorodumi- PDB-4oi3: Crystal structure analysis of SCO4226 from Streptomyces coelicolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oi3 | ||||||
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Title | Crystal structure analysis of 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 | 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 / SCO4226 family nickel-binding protein Function and homology information | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 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 | 4oi3.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oi3.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 4oi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oi3_validation.pdf.gz | 402.9 KB | Display | wwPDB validaton report |
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Full document | 4oi3_full_validation.pdf.gz | 403.4 KB | Display | |
Data in XML | 4oi3_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 4oi3_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oi3 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oi3 | 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: 10211.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO4226 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9FCE4 #2: 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: 1.66 Å3/Da / Density % sol: 25.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M sodium citrate dehydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9794 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2008 |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→34.14 Å / Num. all: 32680 / Num. obs: 30687 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.317 / % possible all: 66.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→34.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.497 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.945 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→34.14 Å
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Refine LS restraints |
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