+Open data
-Basic information
Entry | Database: PDB / ID: 6m25 | ||||||
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Title | Sirohydrochlorin nickelochelatase CfbA in P41 space group | ||||||
Components | Sirohydrochlorin cobaltochelatase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Chelatase | ||||||
Function / homology | Function and homology information sirohydrochlorin nickelchelatase / sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / methanogenesis / cobalt ion binding / nickel cation binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Fujishiro, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Chem Sci / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m25.cif.gz | 61.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m25.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 6m25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m25 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m25 | HTTPS FTP |
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-Related structure data
Related structure data | 6m26C 6m27C 6m28C 6m29C 6m2aC 6m2eC 6m2fC 6m2gC 6m2hC 2xwsS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 1 - 143 / Label seq-ID: 1 - 143
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-Components
#1: Protein | Mass: 16554.045 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Gene: cbiX, cfbA, MJ0970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: Q58380, sirohydrochlorin cobaltochelatase, sirohydrochlorin nickelchelatase #2: Water | ChemComp-HOH / | |
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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: 2.92 Å3/Da / Density % sol: 57.94 % |
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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, 5% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 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: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→68.55 Å / Num. all: 13290 / Num. obs: 13290 / % possible obs: 100 % / Redundancy: 11.8 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.248 / Rsym value: 0.237 / Net I/av σ(I): 2 / Net I/σ(I): 6.9 / Num. measured all: 156207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XWS Resolution: 2.5→68.55 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.438 / SU ML: 0.154 / SU R Cruickshank DPI: 0.0709 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.051 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.33 Å2 / Biso mean: 52.598 Å2 / Biso min: 15.8 Å2
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Refinement step | Cycle: final / Resolution: 2.5→68.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3378 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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