+Open data
-Basic information
Entry | Database: PDB / ID: 6m28 | ||||||
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Title | Sirohydrochlorin nickelochelatase CfbA in complex with Co2+ | ||||||
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: 3 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 | 6m28.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m28.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 6m28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m28 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m28 | HTTPS FTP |
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-Related structure data
Related structure data | 6m25C 6m26C 6m27C 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: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M L-arginine, 0.1M MES, 8% (w/v) gamma-PGA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.74074 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: liquid-nitrogen-cooled Si(111) double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.74074 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→48.17 Å / Num. obs: 7545 / % possible obs: 99.7 % / Redundancy: 26.698 % / Biso Wilson estimate: 90.221 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.073 / Χ2: 0.965 / Net I/σ(I): 34.5 / Num. measured all: 201439 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XWS Resolution: 3→48.17 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.137 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.372 / 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: 190.64 Å2 / Biso mean: 91.222 Å2 / Biso min: 53.58 Å2
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Refinement step | Cycle: final / Resolution: 3→48.17 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3514 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3.001→3.079 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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