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Yorodumi- PDB-5b1h: Crystal structure of cystathionine beta-synthase from Lactobacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b1h | ||||||
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Title | Crystal structure of cystathionine beta-synthase from Lactobacillus plantarum | ||||||
Components | Cystathionine beta-synthase | ||||||
Keywords | LYASE / Enzyme / PLP | ||||||
Function / homology | Function and homology information cystathionine beta-synthase / cystathionine beta-synthase activity / transferase activity, transferring alkyl or aryl (other than methyl) groups / cysteine biosynthetic process from serine Similarity search - Function | ||||||
Biological species | Lactobacillus plantarum WCFS1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Matoba, Y. / Sugiyama, M. | ||||||
Citation | Journal: Protein Sci. / Year: 2017 Title: Crystallographic and mutational analyses of cystathionine beta-synthase in the H2 S-synthetic gene cluster in Lactobacillus plantarum Authors: Matoba, Y. / Yoshida, T. / Izuhara-Kihara, H. / Noda, M. / Sugiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b1h.cif.gz | 249.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b1h.ent.gz | 200.1 KB | Display | PDB format |
PDBx/mmJSON format | 5b1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b1h ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b1h | HTTPS FTP |
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-Related structure data
Related structure data | 5b1iC 2q3dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 33537.008 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria) Strain: WCFS1 / Gene: cbs, lp_0256 / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: F9UT54, cystathionine beta-synthase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: lithium sulfate, hepes |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→100 Å / Num. obs: 62935 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q3D Resolution: 2.4→29.49 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3284001.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.557 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.5 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 2.4→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.54 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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