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Yorodumi- PDB-3b1c: Crystal structure of betaC-S lyase from Streptococcus anginosus: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b1c | ||||||
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Title | Crystal structure of betaC-S lyase from Streptococcus anginosus: Internal aldimine form | ||||||
Components | BetaC-S lyase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding / lyase activity Similarity search - Function | ||||||
Biological species | Streptococcus anginosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Kezuka, Y. / Yoshida, Y. / Nonaka, T. | ||||||
Citation | Journal: Proteins / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b1c.cif.gz | 348.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b1c.ent.gz | 294 KB | Display | PDB format |
PDBx/mmJSON format | 3b1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/3b1c ftp://data.pdbj.org/pub/pdb/validation_reports/b1/3b1c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44649.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus anginosus (bacteria) / Strain: IMU102 / Gene: lcd / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6BMJ3, cystathionine beta-lyase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M Ammonium sulfate, 0.1M Hepes pH7.5, 0.1M Sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 26, 2008 |
Radiation | Monochromator: Fixed exit 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: 1.93→108.47 Å / Num. all: 122200 / Num. obs: 122200 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 |
Reflection shell | Resolution: 1.93→1.97 Å / Rmerge(I) obs: 0.23 / Num. unique all: 7249 / Rsym value: 0.23 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→108.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.679 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 10.729 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→108.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
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