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- PDB-6bxo: Crystal structure of Candidatus Methanoperedens nitroreducens Dph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bxo | ||||||
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Title | Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAH | ||||||
![]() | Diphthamide biosynthesis enzyme Dph2 | ||||||
![]() | BIOSYNTHETIC PROTEIN / DIPHTHAMIDE BIOSYNTHESIS / RADICAL SAM ENZYME | ||||||
Function / homology | ![]() 2-(3-amino-3-carboxypropyl)histidine synthase / 2-(3-amino-3-carboxypropyl)histidine synthase activity / protein histidyl modification to diphthamide / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fenwick, M.K. / Torelli, A.T. / Zhang, Y. / Dong, M. / Kathiresan, V. / Carantoa, J.D. / Dzikovski, B. / Lancaster, K.M. / Freed, J.H. / Hoffman, B.M. ...Fenwick, M.K. / Torelli, A.T. / Zhang, Y. / Dong, M. / Kathiresan, V. / Carantoa, J.D. / Dzikovski, B. / Lancaster, K.M. / Freed, J.H. / Hoffman, B.M. / Lin, H. / Ealick, S.E. | ||||||
![]() | ![]() Title: Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis. Authors: Dong, M. / Kathiresan, V. / Fenwick, M.K. / Torelli, A.T. / Zhang, Y. / Caranto, J.D. / Dzikovski, B. / Sharma, A. / Lancaster, K.M. / Freed, J.H. / Ealick, S.E. / Hoffman, B.M. / Lin, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.4 KB | Display | ![]() |
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PDB format | ![]() | 223.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1004.8 KB | Display | ![]() |
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Full document | ![]() | 1009.4 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bxkC ![]() 6bxlC ![]() 6bxmC ![]() 6bxnC ![]() 3lzcS S: Starting model for refinement C: citing same article ( |
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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: 36459.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ANME2D_01646 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 65 mM HEPES, pH 6.5-7.0, and 18-25% (w/v) polyethylene glycol (PEG) 1000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 67396 / % possible obs: 97.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Rrim(I) all: 0.063 / Χ2: 1.965 / Net I/σ(I): 12.4 / Num. measured all: 210888 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LZC Resolution: 1.655→47.533 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.54 Å2 / Biso mean: 39.1085 Å2 / Biso min: 15.14 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.655→47.533 Å
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Refinement TLS params. | Method: refined / Origin x: 12.7823 Å / Origin y: 17.3084 Å / Origin z: 35.52 Å
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Refinement TLS group | Selection details: not resname HOH |