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Yorodumi- PDB-6zlf: Aerobic crystal structure of F420H2-Oxidase from Methanothermococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zlf | |||||||||
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Title | Aerobic crystal structure of F420H2-Oxidase from Methanothermococcus thermolithotrophicus at 1.8A resolution under 125 bars of krypton | |||||||||
Components | Coenzyme F420H2 oxidase (FprA) | |||||||||
Keywords | OXIDOREDUCTASE / Krypton derivatization / oxidase / O2 | |||||||||
Function / homology | Function and homology information FMN binding / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Methanothermococcus thermolithotrophicus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Engilberge, S. / Wagner, T. / Carpentier, P. / Girard, E. / Shima, S. | |||||||||
Funding support | France, Germany, 2items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2020 Title: Krypton-derivatization highlights O 2 -channeling in a four-electron reducing oxidase. Authors: Engilberge, S. / Wagner, T. / Carpentier, P. / Girard, E. / Shima, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zlf.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zlf.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6zlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zlf_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6zlf_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6zlf_validation.xml.gz | 136.6 KB | Display | |
Data in CIF | 6zlf_validation.cif.gz | 194.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/6zlf ftp://data.pdbj.org/pub/pdb/validation_reports/zl/6zlf | HTTPS FTP |
-Related structure data
Related structure data | 6zk8C 6frmS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
-Protein , 1 types, 8 molecules AFGHIJKL
#1: Protein | Mass: 46242.230 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermococcus thermolithotrophicus (archaea) Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSW8 |
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-Non-polymers , 6 types, 2316 molecules
#2: Chemical | ChemComp-HEZ / #3: Chemical | ChemComp-FEO / #4: Chemical | ChemComp-KR / #5: Chemical | ChemComp-FMN / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Details
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: 2.21 Å3/Da / Density % sol: 44.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris-HCl (pH 8.5) containing 100 mM MgCl2 and 3.3 to 3.7 M hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.4 Å / Num. obs: 294021 / % possible obs: 99.28 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rpim(I) all: 0.035 / Net I/σ(I): 12.84 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 1.07 / Num. unique obs: 29192 / CC1/2: 0.465 / Rpim(I) all: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FRM Resolution: 1.8→48.4 Å / Cross valid method: THROUGHOUT Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 38.71 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→48.4 Å
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Refine LS restraints |
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