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- PDB-8u98: Crystal Structure of Cystathionine beta lyase from Klebsiella aer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8u98 | |||||||||
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Title | Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Glycine adduct) | |||||||||
![]() | Cystathionine beta-lyase | |||||||||
![]() | LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | ![]() L-cysteine catabolic process to pyruvate / cystathionine beta-lyase / : / transsulfuration / pyridoxal phosphate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes (PLP-Glycine adduct) Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Cooper, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 656.6 KB | Display | ![]() |
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PDB format | ![]() | 545.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.2 MB | Display | ![]() |
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Full document | ![]() | 4.2 MB | Display | |
Data in XML | ![]() | 69.7 KB | Display | |
Data in CIF | ![]() | 104.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 44102.242 Da / Num. of mol.: 4 / Mutation: V244I, L360P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: EAE_03480 / Plasmid: KlaeA.00906.a.B1 / Production host: ![]() ![]() #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-GLY / #4: Chemical | ChemComp-EDO / #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: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus E6: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM HEPES/MOPS, pH 7.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene ...Details: Morpheus E6: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM HEPES/MOPS, pH 7.5, 30 mM Diethylene glycol, 30 mM Triethyleneglycol, 30 mM Tetraethylene glycol and 30 mM Pentaethylene glycol, 2mM PLP and glycine added to the protein prior to crystallization, KlaeA.00906.a.B1.PW39169 at 41.1 mg/mL. Plate: 13534 well E6 drop 2, Puck: PSL-0903, Cryo: Direct |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 6, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→102.43 Å / Num. obs: 359218 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Χ2: 1.01 / Net I/σ(I): 15.4 / Num. measured all: 2484245 |
Reflection shell | Resolution: 1.4→1.44 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.018 / Num. measured all: 185109 / Num. unique obs: 26567 / CC1/2: 0.809 / Rpim(I) all: 0.414 / Rrim(I) all: 1.1 / Χ2: 1.04 / Net I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→24.82 Å
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Refine LS restraints |
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LS refinement shell |
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