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Yorodumi- PDB-6qp2: Crystal structure of the PLP-bound C-S lyase from Staphylococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qp2 | ||||||
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Title | Crystal structure of the PLP-bound C-S lyase from Staphylococcus hominis | ||||||
Components |
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Keywords | LYASE / pyridoxal phosphate binding / Cysteine-S-conjugate beta-lyase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus hominis (bacteria) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 6qp2.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qp2.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/6qp2 ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qp2 | HTTPS FTP |
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-Related structure data
Related structure data | 6qp1C 6qp3C 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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Unit cell |
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-Components
#1: Protein | Mass: 48428.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Contains a lysine covalently attached to a PLP molecule at position 246. In addition to the protein sequence, this entity also contains additional residues introduced by the expression ...Details: Contains a lysine covalently attached to a PLP molecule at position 246. In addition to the protein sequence, this entity also contains additional residues introduced by the expression vector. (MGGGFA.....ENLYFQGHHHHHHHHHH) Source: (gene. exp.) Staphylococcus hominis (bacteria) / Gene: BUZ46_10400 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A533IVU2*PLUS #2: Protein/peptide | | Mass: 846.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Polyhistidine from tag introduced by expression vector but from unknown monomer. Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli MC1061 (bacteria) #3: Chemical | #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: 1.88 Å3/Da / Density % sol: 34.58 % / Description: Long flat yellow shards. |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 4% Tacsimate pH 6.0, 12% PEG 3,350 (F1: PEG/ION HT) |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→52.4 Å / Num. obs: 97945 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.105 / Net I/σ(I): 11.4 / Num. measured all: 784938 / Scaling rejects: 11 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.628 / Num. unique obs: 4791 / CC1/2: 0.336 / Rpim(I) all: 0.973 / Rrim(I) all: 2.805 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DQ6 Resolution: 1.6→52.4 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.922 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.51 Å2 / Biso mean: 29.66 Å2 / Biso min: 15.8 Å2
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Refinement step | Cycle: final / Resolution: 1.6→52.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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