+Open data
-Basic information
Entry | Database: PDB / ID: 6qvh | ||||||
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Title | Streptomyces lividans Ccsp mutant - H113A | ||||||
Components | cytosolic copper storage protein | ||||||
Keywords | METAL BINDING PROTEIN / Copper / Streptomyces lividans / storage / homeostasis / toxicity | ||||||
Function / homology | Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / COPPER (I) ION / Four-helix bundle copper-binding protein Function and homology information | ||||||
Biological species | Streptomyces lividans 1326 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å | ||||||
Authors | Straw, M.L. / Hough, M.A. | ||||||
Citation | Journal: Chemistry / Year: 2019 Title: A Histidine Residue and a Tetranuclear Cuprous-thiolate Cluster Dominate the Copper Loading Landscape of a Copper Storage Protein from Streptomyces lividans. Authors: Straw, M.L. / Hough, M.A. / Wilson, M.T. / 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 | 6qvh.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qvh.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/6qvh ftp://data.pdbj.org/pub/pdb/validation_reports/qv/6qvh | HTTPS FTP |
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-Related structure data
Related structure data | 6q58C 6q6bC 6qybC 6r01C 6ei0S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13128.985 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SCO3281 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X8F4 | ||
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#2: Chemical | ChemComp-CU1 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: between and 10-15 mg/ml of protein mixed with 1.5 M Ammonium sulfate, 0.1M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→32.67 Å / Num. obs: 33353 / % possible obs: 96.7 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.04 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1526 / CC1/2: 0.586 / Rpim(I) all: 0.566 / Rrim(I) all: 1.554 / % possible all: 89.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EI0 Resolution: 1.28→32.67 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.224 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.16 Å2 / Biso mean: 31.84 Å2 / Biso min: 15.46 Å2
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Refinement step | Cycle: final / Resolution: 1.28→32.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.28→1.313 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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