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Yorodumi- PDB-8iof: Crystal structure of N-methyl-Cis-4-hydroxy-D-proline dehydratase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iof | ||||||
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Title | Crystal structure of N-methyl-Cis-4-hydroxy-D-proline dehydratase in Clostridium sp. FS41 | ||||||
Components | Benzylsuccinate synthase alpha subunit | ||||||
Keywords | LYASE / Glycyl Radical Enzyme / dehydratase / N-methyl-Cis-4-hydroxy-D-proline | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium sp. FS41 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Jiang, L. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of N-methyl-Cis-4-hydroxy-D-proline dehydratase in Clostridium sp. FS41 Authors: Jiang, L. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iof.cif.gz | 631.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iof.ent.gz | 518.9 KB | Display | PDB format |
PDBx/mmJSON format | 8iof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/8iof ftp://data.pdbj.org/pub/pdb/validation_reports/io/8iof | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 89175.391 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium sp. FS41 (bacteria) / Gene: bssA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F0CL90 #2: Chemical | ChemComp-87I / ( Mass: 145.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO3 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | 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: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M Bis-Tris propane, pH 6.5, 16% (w/v) PEG3350, 100 mM cis-N-Methyl-4-hydroxy-D-proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→39.49 Å / Num. obs: 144785 / % possible obs: 98.4 % / Redundancy: 3.3 % / CC1/2: 0.75 / Χ2: 0.63 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 2.33→2.39 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.261 / Num. unique obs: 10653 / CC1/2: 0.246 / Rpim(I) all: 0.896 / Rrim(I) all: 0.99 / Χ2: 0.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→39.427 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 0.09 / Phase error: 28.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→39.427 Å
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Refine LS restraints |
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LS refinement shell |
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