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- PDB-7c6o: Catalytic Subunit of Cobaltochelatase from Mycobacterium tuberculosis -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c6o | |||||||||
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Title | Catalytic Subunit of Cobaltochelatase from Mycobacterium tuberculosis | |||||||||
![]() | Cobalamin biosynthesis protein CobN | |||||||||
![]() | LIGASE / Co-CHELATASE / METAL BINDING PROTEIN | |||||||||
Function / homology | ![]() cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, J. / Liu, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis. Authors: Zhang, J.H. / Yuan, H. / Wang, X. / Dai, H.E. / Zhang, M. / Liu, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 500.5 KB | Display | ![]() |
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PDB format | ![]() | 402.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
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Full document | ![]() | 454.3 KB | Display | |
Data in XML | ![]() | 49.5 KB | Display | |
Data in CIF | ![]() | 74.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zhjS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 133181.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cobN, DSI38_03330, ERS023446_03562, ERS094182_01916, F6W99_00653, GJE03_10820 Production host: ![]() ![]() References: UniProt: A0A0T5XW27, UniProt: O53498*PLUS, cobaltochelatase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.92 % |
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Crystal grow | Temperature: 289 K / Method: liquid diffusion / Details: PEG 10,000, Ethylene glycol, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 110491 / % possible obs: 97.1 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique obs: 10924 / CC1/2: 0.743 / Rpim(I) all: 0.47 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZHJ Resolution: 1.801→48.501 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.92 / 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 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.33 Å2 / Biso mean: 24.3623 Å2 / Biso min: 8.43 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→48.501 Å
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Refinement TLS params. | Method: refined / Origin x: -24.531 Å / Origin y: -4.954 Å / Origin z: -31.648 Å
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Refinement TLS group | Selection details: all |