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- PDB-6ldo: Crystal structure of cystathionine gamma-lyase from Lactobacillus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ldo | ||||||
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Title | Crystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with L-serine | ||||||
![]() | Cystathionine gamma-lyase | ||||||
![]() | LYASE / cystathionine gamma-lyase | ||||||
Function / homology | ![]() cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-synthase activity / : / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / transaminase activity ...cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-synthase activity / : / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / transaminase activity / pyridoxal phosphate binding / lyase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oda, K. / Matoba, Y. | ||||||
![]() | ![]() Title: Catalytic specificity of the Lactobacillus plantarum cystathionine gamma-lyase presumed by the crystallographic analysis. Authors: Matoba, Y. / Noda, M. / Yoshida, T. / Oda, K. / Ezumi, Y. / Yasutake, C. / Izuhara-Kihara, H. / Danshiitsoodol, N. / Kumagai, T. / Sugiyama, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 443.1 KB | Display | ![]() |
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PDB format | ![]() | 364.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 84.6 KB | Display | |
Data in CIF | ![]() | 117.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6le4C ![]() 4l0oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 41915.562 Da / Num. of mol.: 6 / Mutation: K194A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-KOU / ( #3: Chemical | ChemComp-PO4 / #4: 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: 4.42 Å3/Da / Density % sol: 72.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: KH2PO4, NaH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.743→100 Å / Num. obs: 112736 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.065 / Rrim(I) all: 0.127 / Χ2: 1.006 / Net I/σ(I): 6.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 4L0O Resolution: 2.75→35.682 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 257.65 Å2 / Biso mean: 42.2282 Å2 / Biso min: 16.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→35.682 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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