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Yorodumi- PDB-3pft: Crystal Structure of Untagged C54A Mutant Flavin Reductase (DszD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pft | ||||||
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Title | Crystal Structure of Untagged C54A Mutant Flavin Reductase (DszD) in Complex with FMN From Mycobacterium goodii | ||||||
Components | Flavin reductase | ||||||
Keywords | OXIDOREDUCTASE / Flavin Reductase / Desulfurization | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium goodii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Li, Q. / Xu, P. / Ma, C. / Gu, L. / Liu, X. / Zhang, C. / Li, N. / Su, J. / Li, B. / Liu, S. | ||||||
Citation | Journal: To be Published Title: The flavin reductase DSZD from a desulfurizing mycobacterium goodii strain: systemic manipulation and investigation based on the crystal structure Authors: Li, Q. / Xu, P. / Ma, C. / Gu, L. / Liu, X. / Zhang, C. / Li, N. / Su, J. / Li, B. / Liu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pft.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pft.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pft_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3pft_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3pft_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3pft_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/3pft ftp://data.pdbj.org/pub/pdb/validation_reports/pf/3pft | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 16472.627 Da / Num. of mol.: 2 / Fragment: UNP residues 5-161 / Mutation: C54A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium goodii (bacteria) / Strain: X7B / Gene: dszD / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6CDL6, EC: 1.5.1.29 #2: Chemical | #3: 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: 2.85 Å3/Da / Density % sol: 56.91 % / Mosaicity: 0.263 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris, 34% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 49333 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.059 / Χ2: 1.204 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→35.058 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8869 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.12 / 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 / Bsol: 63.609 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.47 Å2 / Biso mean: 23.5352 Å2 / Biso min: 9.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.601→35.058 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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