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Yorodumi- PDB-6qp3: Crystal structure of the PLP-bound C-S lyase from Bacillus subtil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qp3 | ||||||
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Title | Crystal structure of the PLP-bound C-S lyase from Bacillus subtilis (strain 168) | ||||||
Components | Cystathionine beta-lyase PatB | ||||||
Keywords | LYASE / pyridoxal phosphate binding / Cysteine-S-conjugate beta-lyase | ||||||
Function / homology | Function and homology information cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / : / methionine biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Herman, R. / Rudden, M. / Wilkinson, A.J. / Hanai, S. / Thomas, G.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: The molecular basis of thioalcohol production in human body odour. Authors: Rudden, M. / Herman, R. / Rose, M. / Bawdon, D. / Cox, D.S. / Dodson, E. / Holden, M.T.G. / Wilkinson, A.J. / James, A.G. / Thomas, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qp3.cif.gz | 299.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qp3.ent.gz | 243.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/6qp3 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qp3 | HTTPS FTP |
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-Related structure data
Related structure data | 6qp1C 6qp2C 4dq6S 6rvi 6rvj 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42838.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: patB, BSU31440 / Production host: Escherichia coli MC1061 (bacteria) References: UniProt: Q08432, cysteine-S-conjugate beta-lyase #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PLP / #4: 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.2M Ammonium acetate, 20% PEG 3,350, pH 7.1 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→61.28 Å / Num. obs: 72159 / % possible obs: 96.1 % / Redundancy: 7.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.071 / Rrim(I) all: 0.21 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.195 / Num. unique obs: 3803 / CC1/2: 0.574 / Rpim(I) all: 0.479 / Rrim(I) all: 1.295 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DQ6 Resolution: 2.3→61.28 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.48 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.257 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.43 Å2 / Biso mean: 27.599 Å2 / Biso min: 11.45 Å2
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Refinement step | Cycle: final / Resolution: 2.3→61.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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