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Yorodumi- PDB-8cns: The Hybrid Cluster Protein from the thermophilic methanogen Metha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cns | |||||||||
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Title | The Hybrid Cluster Protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus in a mixed redox state after soaking with hydroxylamine, at 1.36-A resolution. | |||||||||
Components | Hybrid cluster protein from Methanothermococcus thermolithotrophicus | |||||||||
Keywords | OXIDOREDUCTASE / Hybrid cluster / prismane protein / Hybrid cluster protein / methanogenic archaea / anaerobic biochemistry / thermophile / metallocluster / Nitric oxide reductase / hydroxylamine | |||||||||
Function / homology | ACETATE ION / FORMIC ACID / HYDROXYAMINE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / hybrid cluster Function and homology information | |||||||||
Biological species | Methanothermococcus thermolithotrophicus DSM 2095 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | |||||||||
Authors | Lemaire, O.N. / Wagner, T. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Front Microbiol / Year: 2023 Title: Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Authors: Lemaire, O.N. / Belhamri, M. / Wagner, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cns.cif.gz | 263.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cns.ent.gz | 213.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cns_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8cns_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8cns_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 8cns_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/8cns ftp://data.pdbj.org/pub/pdb/validation_reports/cn/8cns | HTTPS FTP |
-Related structure data
Related structure data | 8cnrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60367.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Compared to the automatic annotation, the sequence has a five-residue extension in its N-terminal (MRPSK). The cysteine 402 has a thiol addition in its oxidized state. Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: hydroxylamine reductase |
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-Non-polymers , 14 types, 666 molecules
#2: Chemical | ChemComp-HOA / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-SF4 / | #6: Chemical | ChemComp-SF3 / | #7: Chemical | ChemComp-PEG / | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-PG5 / | #10: Chemical | ChemComp-GOL / | #11: Chemical | ChemComp-TRS / | #12: Chemical | ChemComp-VQ8 / | #13: Chemical | ChemComp-ACT / #14: Chemical | ChemComp-MRD / ( | #15: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.41 Å3/Da / Density % sol: 49.06 % Description: Brown orthorhombic rod. Appeared after few weeks. |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Crystallisation was performed anaerobically by initial screening at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a ...Details: Crystallisation was performed anaerobically by initial screening at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a N2/H2 (97:3%) atmosphere. The reservoir chamber was filled with 90 ul of crystallisation condition, and the crystallisation drop was formed by spotting 0.55 ul protein with 0.55 ul of 20% (w/v) PEG 3,350 and 200 mM Magnesium formate. The protein was crystallised at 9.9 mg/ml in 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% (v/v) glycerol. Densities in the electron density map suggest a contamination of another crystallisation condition spatially close and containing 30% (v/v) 2-Methyl-2,4-pentanediol, 20 mM Calcium chloride and 100 mM Sodium acetate, pH 4.6. The crystal was soaked for 5.7 min in a solution of 100 mM hydroxylamine/HCl in the crystallisation condition and then soaked in the crystallisation solution supplemented with 20% v/v ethylene glycol for a few seconds before freezing in liquid nitrogen. PH range: / / Temp details: / |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0004 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 1.356→70.645 Å / Num. obs: 89372 / % possible obs: 94.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.043 / Rrim(I) all: 0.118 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.356→1.476 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4469 / CC1/2: 0.611 / Rpim(I) all: 0.472 / Rrim(I) all: 1.165 / % possible all: 67.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→51.09 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.74 / Stereochemistry target values: ML Details: Refinement steps were performed by considering all atoms anisotropic. The model was refined with hydrogens in riding position. Hydrogens were omitted in the final deposited model.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→51.09 Å
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Refine LS restraints |
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LS refinement shell |
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