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- PDB-6ld9: Crystal structure of cystathionine gamma synthase from Xanthomona... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ld9 | ||||||
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Title | Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with cystathionine | ||||||
![]() | Cystathionine gamma-synthase | ||||||
![]() | BIOSYNTHETIC PROTEIN / cysathionine gamma synthase / PLP dependent enzyme / methionine biosynthesis pathway | ||||||
Function / homology | ![]() carbon-sulfur lyase activity / cystathionine gamma-synthase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ngo, H.P.T. / Nguyen, T.D.Q. / Kang, L.W. | ||||||
![]() | ![]() Title: Crystal structure of cystathionine gamma synthase from Xanthomonas oryzae pv. oryzae in complex with cystathionine Authors: Ngo, H.P.T. / Nguyen, T.D.Q. / Kang, L.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 574.5 KB | Display | ![]() |
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PDB format | ![]() | 476.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 60.5 KB | Display | |
Data in CIF | ![]() | 83.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ld7S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43168.809 Da / Num. of mol.: 4 / Mutation: D5Y, H8D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: KACC10331 / Gene: metB, XOO1818 / Production host: ![]() ![]() #2: Chemical | ChemComp-E9U / ( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.74 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.12 M Ethylene Glycols Mix, 0.1 M Na HEPES/MOPS pH 7.5, 10%(w/v) PEG 4000, 20%(v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 106893 / % possible obs: 99.76 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 10462 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LD7 Resolution: 2.5→47.06 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.36 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 112.7 Å2 / Biso mean: 30.917 Å2 / Biso min: 14.91 Å2
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Refinement step | Cycle: final / Resolution: 2.5→47.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.503→2.568 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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