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- PDB-3b1d: Crystal structure of betaC-S lyase from Streptococcus anginosus i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b1d | ||||||
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Title | Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: External aldimine form | ||||||
![]() | BetaC-S lyase | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding / lyase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kezuka, Y. / Yoshida, Y. / Nonaka, T. | ||||||
![]() | ![]() Title: Structural insights into catalysis by beta C-S lyase from Streptococcus anginosus Authors: Kezuka, Y. / Yoshida, Y. / Nonaka, T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and preliminary X-ray analysis of betaC-S lyases from two oral Streptococci Authors: Kezuka, Y. / Yoshida, Y. / Nonaka, T. #2: Journal: Oral Microbiol.Immunol. / Year: 2008 Title: Molecular and enzymatic characterization of betaC-S lyase in Streptococcus constellatus Authors: Yoshida, Y. / Ito, S. / Sasaki, T. / Kishi, M. / Kurota, M. / Suwabe, A. / Kunimatsu, K. / Kato, H. #3: Journal: Biochem.Biophys.Res.Commun. / Year: 2003 Title: Differences in the betaC-S lyase activities of viridans group streptococci Authors: Yoshida, Y. / Negishi, M. / Amano, A. / Oho, T. / Nakano, Y. #4: Journal: Microbiology / Year: 2002 Title: lcd from Streptococcus anginosus encodes a C-S lyase with alpha,beta-elimination activity that degrades L-cysteine Authors: Yoshida, Y. / Nakano, Y. / Amano, A. / Yoshimura, M. / Fukamachi, H. / Oho, T. / Koga, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358.8 KB | Display | ![]() |
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PDB format | ![]() | 302.5 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 | ![]() | 74 KB | Display | |
Data in CIF | ![]() | 108.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44649.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1637 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/PLS.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLS.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PLS / [ #4: Chemical | ChemComp-EPE / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 8000, 0.1M Hepes pH7.5, 0.08M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2008 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→36.84 Å / Num. all: 189945 / Num. obs: 189945 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.66→1.7 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.1 / Num. unique all: 13790 / Rsym value: 0.248 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 9.178 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→36.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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