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Yorodumi- PDB-7bqw: Crystal structure of Methionine gamma-lyase from Fusobacterium nu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bqw | |||||||||
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Title | Crystal structure of Methionine gamma-lyase from Fusobacterium nucleatum | |||||||||
Components | L-methionine gamma-lyase | |||||||||
Keywords | LYASE / Methionine gamma-lyase / Fn1419 / Fusobacterium nucleatum | |||||||||
Function / homology | Function and homology information L-cysteine desulfidase / homocysteine desulfhydrase / homocysteine desulfhydrase activity / carbon-sulfur lyase activity / methionine gamma-lyase / methionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Lan, J. / Chen, Y. / Liu, W. / Xu, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Methionine gamma-lyase from Fusobacterium nucleatum Authors: Lan, J. / Liu, W. / Chen, Y. / Xu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bqw.cif.gz | 340.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bqw.ent.gz | 221.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/7bqw ftp://data.pdbj.org/pub/pdb/validation_reports/bq/7bqw | HTTPS FTP |
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-Related structure data
Related structure data | 5dx5S 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
#1: Protein | Mass: 43357.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria) Gene: FN1419 / Production host: Escherichia coli (E. coli) References: UniProt: Q8RDT4, methionine gamma-lyase, homocysteine desulfhydrase, L-cysteine desulfidase #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: 2.28 Å3/Da / Density % sol: 46.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 20% PEG 5000, 0.2M sodium formate, 0.1M BICINE pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 56011 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 47.74 Å2 / Rsym value: 0.07 / Net I/σ(I): 23.77 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 55899 / Rsym value: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DX5 Resolution: 2.5→48.75 Å / SU ML: 0.3658 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5913
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.75 Å
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Refine LS restraints |
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LS refinement shell |
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