+Open data
-Basic information
Entry | Database: PDB / ID: 8ytr | ||||||
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Title | The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus | ||||||
Components | CopC domain-containing protein | ||||||
Keywords | METAL BINDING PROTEIN / CopC / Copper resistance protein C / Copper chaperone / Cu(II)-loaded / Holo-form | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thioalkalivibrio paradoxus ARh 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kulikova, O.G. / Solovieva, A.Y. / Varfolomeeva, L.A. / Dergousova, N.I. / Nikolaeva, A.Y. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus Authors: Kulikova, O.G. / Solovieva, A.Y. / Varfolomeeva, L.A. / Dergousova, N.I. / Nikolaeva, A.Y. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ytr.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ytr.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ytr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ytr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ytr_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ytr_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 8ytr_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/8ytr ftp://data.pdbj.org/pub/pdb/validation_reports/yt/8ytr | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14036.403 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria) Gene: THITH_13340 / Production host: Escherichia coli (E. coli) / References: UniProt: W0DSL1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.02 Å3/Da / Density % sol: 38.96 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion / Details: 0.2M Ammonium formate pH 6.6, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→104.66 Å / Num. obs: 21085 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.054 / Rrim(I) all: 0.14 / Χ2: 0.84 / Net I/σ(I): 6.4 / Num. measured all: 137790 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible obs: 99.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.735 / Num. measured all: 8112 / Num. unique obs: 1238 / CC1/2: 0.858 / Rpim(I) all: 0.307 / Rrim(I) all: 0.798 / Χ2: 0.73 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→52.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.994 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 30.966 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→52.39 Å
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Refine LS restraints |
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