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Yorodumi- PDB-4bpy: Crystal structure of the C90A mutant of the Sco copper chaperone ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bpy | ||||||
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Title | Crystal structure of the C90A mutant of the Sco copper chaperone protein from Streptomyces lividans | ||||||
Components | SCO PROTEIN | ||||||
Keywords | CHAPERONE / COPPER HOMEOSTASIS / HOMEOSTASIS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES LIVIDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Blundell, K.L.I.M. / Hough, M.A. / Worrall, J.A.R. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Structural and Mechanistic Insights Into an Extracytoplasmic Copper Trafficking Pathway in Streptomyces Lividans. Authors: Blundell, K.L.I.M. / Hough, M.A. / Vijgenboom, E. / Worrall, J.A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bpy.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bpy.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bpy_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 4bpy_full_validation.pdf.gz | 425.3 KB | Display | |
Data in XML | 4bpy_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 4bpy_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bpy ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bpy | HTTPS FTP |
-Related structure data
Related structure data | 3zjaC 3zk0C 2b7kS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 19059.484 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q93J40, UniProt: A0A7U9HC27*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | TRUNCATED CONSTRUCT BEGINNING WITH RESIDUE 42 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 37.9 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: 28 % PEG 4000, 0.05 M NAAC PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→35.7 Å / Num. obs: 28622 / % possible obs: 99.8 % / Observed criterion σ(I): 100 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B7K Resolution: 1.4→35.68 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.564 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ANISOTROPIC BS
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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: 20.786 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→35.68 Å
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Refine LS restraints |
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