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- PDB-6m2a: A non-His-rich type of chimeric sirohydrochlorin nickelochelatase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m2a | ||||||
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Title | A non-His-rich type of chimeric sirohydrochlorin nickelochelatase CfbA from M. jannaschii and M. barkeri | ||||||
![]() | Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase,Sirohydrochlorin cobaltochelatase | ||||||
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Function / homology | ![]() sirohydrochlorin nickelchelatase / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujishiro, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis. Authors: Fujishiro, T. / Ogawa, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.8 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6m25C ![]() 6m26C ![]() 6m27C ![]() 6m28C ![]() 6m29C ![]() 6m2eC ![]() 6m2fC ![]() 6m2gC ![]() 6m2hC ![]() 2xwsS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 1 - 126 / Label seq-ID: 1 - 126
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Components
#1: Protein | Mass: 14015.420 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: This chimeric protein was prepared by substitution of the His-rich region of CfbA from Methanocaldococcus jannaschii by the corresponding non-His-rich region of CfbA from Methanosarcina barkeri. Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Gene: cbiX, cfbA, MJ0970, cbiX, cfbA / Production host: ![]() ![]() ![]() References: UniProt: Q58380, UniProt: P61816, ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.1M ammonium sulfate, 0.3M Na-formate, 0.1M Tris, 3% (w/v) gamma-PGA, 10% (w/v) PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.23→43.48 Å / Num. obs: 12499 / % possible obs: 99.7 % / Redundancy: 9.289 % / Biso Wilson estimate: 45.688 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rrim(I) all: 0.184 / Χ2: 0.926 / Net I/σ(I): 8.56 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2XWS Resolution: 2.23→43.48 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 2.38 / Phase error: 23.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.51 Å2 / Biso mean: 43.5316 Å2 / Biso min: 22.51 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→43.48 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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