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Yorodumi- PDB-3e6g: Crystal structure of XometC, a cystathionine c-lyase-like protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e6g | ||||||
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Title | Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae | ||||||
Components | Cystathionine gamma-lyase-like protein | ||||||
Keywords | LYASE / Bacterial blight / cystathionine lyase / reverse transsulfuration pathway / Xanthomonas oryzae pv.oryzae | ||||||
Function / homology | Function and homology information carbon-sulfur lyase activity / cystathionine gamma-synthase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Xanthomonas oryzae pv. oryzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ngo, H.P.T. / Kim, J.K. / Kim, H.S. / Jung, J.H. / Ahn, Y.J. / Kim, J.G. / Lee, B.M. / Kang, H.W. / Kang, L.W. | ||||||
Citation | Journal: To be published Title: Crystal structure of XometC, a cystathionine c-lyase-like protein from Xanthomonas oryzae pv.oryzae Authors: Ngo, H.P.T. / Kim, J.K. / Kim, H.S. / Jung, J.H. / Ahn, Y.J. / Kim, J.G. / Lee, B.M. / Kang, H.W. / Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e6g.cif.gz | 267.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e6g.ent.gz | 217 KB | Display | PDB format |
PDBx/mmJSON format | 3e6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e6g_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
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Full document | 3e6g_full_validation.pdf.gz | 515.8 KB | Display | |
Data in XML | 3e6g_validation.xml.gz | 54 KB | Display | |
Data in CIF | 3e6g_validation.cif.gz | 73.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/3e6g ftp://data.pdbj.org/pub/pdb/validation_reports/e6/3e6g | HTTPS FTP |
-Related structure data
Related structure data | 2i87S 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: 42917.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria) Gene: metB, XOO0778 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H4T8 #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: 2.69 Å3/Da / Density % sol: 54.29 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG3350, 0.2M lithium sulfate monohydrate, 0.1M bis-Tris, pH5.5, sodium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2008 |
Radiation | Monochromator: flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 44441 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I87 Resolution: 2.8→42.26 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.872 / SU B: 16.079 / SU ML: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 52.296 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→42.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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