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- PDB-7d7o: Crystal structure of cystathionine gamma-lyase from Bacillus cere... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d7o | ||||||
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Title | Crystal structure of cystathionine gamma-lyase from Bacillus cereus ATCC 14579 | ||||||
![]() | Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase | ||||||
![]() | BIOSYNTHETIC PROTEIN / cysteine / PLP-dependent enzyme | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sagong, H.-Y. / Kim, B. / Kim, K.-J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Functional Characterization of Cystathionine gamma-lyase from Bacillus cereus ATCC 14579. Authors: Sagong, H.Y. / Kim, B. / Joo, S. / Kim, K.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.4 KB | Display | ![]() |
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PDB format | ![]() | 124.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6khqS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41320.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: EJ379_22345 Production host: ![]() ![]() References: UniProt: A0A5B7VKY7 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: 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: 3.06 Å3/Da / Density % sol: 59.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2M Ammonium sulfate, 0.1 M Tris-HCl (pH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 71253 / % possible obs: 93.7 % / Redundancy: 11.8 % / CC1/2: 1 / Net I/σ(I): 35.02 |
Reflection shell | Resolution: 1.98→2.01 Å / Num. unique obs: 3186 / CC1/2: 0.505 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KHQ Resolution: 1.98→33.04 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.454 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.166 / 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: 123.02 Å2 / Biso mean: 40.012 Å2 / Biso min: 21.12 Å2
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Refinement step | Cycle: final / Resolution: 1.98→33.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.982→2.034 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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