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Yorodumi- PDB-5x41: 3.5A resolution structure of a cobalt energy-coupling factor tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x41 | ||||||
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Title | 3.5A resolution structure of a cobalt energy-coupling factor transporter using LCP method-CbiMQO | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / CbiMQO / ECF transporter / LCP | ||||||
Function / homology | Function and homology information cobalt ion transport / cobalt ion transmembrane transporter activity / cobalamin biosynthetic process / plasma membrane => GO:0005886 / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.47 Å | ||||||
Authors | Bao, Z. / Qi, X. / Zhao, W. / Li, D. / Zhang, P. | ||||||
Citation | Journal: Cell Res. / Year: 2017 Title: Structure and mechanism of a group-I cobalt energy coupling factor transporter Authors: Bao, Z. / Qi, X. / Hong, S. / Xu, K. / He, F. / Zhang, M. / Chen, J. / Chao, D. / Zhao, W. / Li, D. / Wang, J. / Zhang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x41.cif.gz | 708.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x41.ent.gz | 594.9 KB | Display | PDB format |
PDBx/mmJSON format | 5x41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/5x41 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/5x41 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29464.053 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7HZ57*PLUS #2: Protein | Mass: 22554.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: cbiM / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q0R232 #3: Protein | Mass: 27228.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7HYD7*PLUS |
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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: 3.05 Å3/Da / Density % sol: 59.7 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: 0.1M NaCl, 35-48% PEG 400, 0.1M MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.47→50 Å / Num. obs: 34336 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.3 |
-Processing
Software |
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Refinement | Resolution: 3.47→47.962 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.51 / 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: 3.47→47.962 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -75.523 Å / Origin y: 129.1001 Å / Origin z: 425.3314 Å
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Refinement TLS group | Selection details: all |