+Open data
-Basic information
Entry | Database: PDB / ID: 8ytq | ||||||
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Title | The structure of apoCopC from Thioalkalivibrio paradoxus | ||||||
Components | CopC domain-containing protein | ||||||
Keywords | METAL BINDING PROTEIN / CopC / Copper resistance protein C / Apo-form / Copper chaperone / Thioalkalivibrio paradoxus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thioalkalivibrio paradoxus ARh 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kulikova, O.G. / Solovieva, A.Y. / Varfolomeeva, L.A. / Dergousova, N.I. / 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 apoCopC from Thioalkalivibrio paradoxus Authors: Kulikova, O.G. / Solovieva, A.Y. / Varfolomeeva, L.A. / Dergousova, N.I. / 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 | 8ytq.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ytq.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ytq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ytq_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8ytq_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8ytq_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 8ytq_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/8ytq ftp://data.pdbj.org/pub/pdb/validation_reports/yt/8ytq | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 14036.403 Da / Num. of mol.: 4 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: Chemical | #5: 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: 2.05 Å3/Da / Density % sol: 40.09 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55.35 Å / Num. obs: 47498 / % possible obs: 98.2 % / Redundancy: 4.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.048 / Rrim(I) all: 0.099 / Χ2: 0.93 / Net I/σ(I): 7.7 / Num. measured all: 194184 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 95.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.612 / Num. measured all: 10364 / Num. unique obs: 2495 / CC1/2: 0.814 / Rpim(I) all: 0.336 / Rrim(I) all: 0.7 / Χ2: 0.9 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→55.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.562 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.157 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→55.35 Å
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Refine LS restraints |
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