+Open data
-Basic information
Entry | Database: PDB / ID: 4xa7 | ||||||
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Title | Soluble part of holo NqrC from V. harveyi | ||||||
Components | Na(+)-translocating NADH-quinone reductase subunit C | ||||||
Keywords | OXIDOREDUCTASE / Na+-translocating NADH:quinone oxidoreductase / redox-driven sodium pump | ||||||
Function / homology | FLAVIN MONONUCLEOTIDE / : Function and homology information | ||||||
Biological species | Vibrio harveyi CAIM 1792 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Borshchevskiy, V. / Round, E. / Bertsova, Y. / Polovinkin, V. / Gushchin, I. / Mishin, A. / Kovalev, K. / Kachalova, G. / Popov, A. / Bogachev, A. / Gordeliy, V. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Structural and Functional Investigation of Flavin Binding Center of the NqrC Subunit of Sodium-Translocating NADH:Quinone Oxidoreductase from Vibrio harveyi. Authors: Borshchevskiy, V. / Round, E. / Bertsova, Y. / Polovinkin, V. / Gushchin, I. / Ishchenko, A. / Kovalev, K. / Mishin, A. / Kachalova, G. / Popov, A. / Bogachev, A. / Gordeliy, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xa7.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xa7.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 4xa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xa7_validation.pdf.gz | 758.6 KB | Display | wwPDB validaton report |
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Full document | 4xa7_full_validation.pdf.gz | 759.1 KB | Display | |
Data in XML | 4xa7_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 4xa7_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/4xa7 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xa7 | HTTPS FTP |
-Related structure data
Related structure data | 3lwxS S: Starting model for refinement |
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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: 27553.756 Da / Num. of mol.: 1 / Fragment: UNP residues 33-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi CAIM 1792 (bacteria) / Gene: nqrC, MUQ_18848 / Production host: Escherichia coli (E. coli) References: UniProt: M7R347, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M K thiocyanate, 20-30%(w/v) PEG MME 2000 / PH range: 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→46.53 Å / Num. all: 28742 / Num. obs: 27755 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 0.63 / % possible all: 74.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LWX Resolution: 1.56→46.53 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→46.53 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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