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Yorodumi- PDB-6c2q: Crystal Structures of Cystathionine beta-Synthase from Saccharomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c2q | ||||||
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Title | Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-L-Serine Intermediate | ||||||
Components | Cystathionine beta-synthaseCystathionine beta synthase | ||||||
Keywords | LYASE / CBS / synthase / PLP | ||||||
Function / homology | Function and homology information Cysteine formation from homocysteine / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / hydrogen sulfide biosynthetic process / traversing start control point of mitotic cell cycle / cysteine biosynthetic process from serine / transsulfuration / cytoplasmic stress granule / mRNA binding ...Cysteine formation from homocysteine / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / hydrogen sulfide biosynthetic process / traversing start control point of mitotic cell cycle / cysteine biosynthetic process from serine / transsulfuration / cytoplasmic stress granule / mRNA binding / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Kreinbring, C.A. / Tu, Y. / Liu, D. / Petsko, G.A. / Ringe, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. Authors: Tu, Y. / Kreinbring, C.A. / Hill, M. / Liu, C. / Petsko, G.A. / McCune, C.D. / Berkowitz, D.B. / Liu, D. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c2q.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c2q.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 6c2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/6c2q ftp://data.pdbj.org/pub/pdb/validation_reports/c2/6c2q | HTTPS FTP |
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-Related structure data
Related structure data | 6c2hC 6c2zC 6c4pC 1jbqS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41286.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CYS4, STR4, YGR155W, G6667 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) / References: UniProt: P32582, cystathionine beta-synthase |
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-Non-polymers , 8 types, 163 molecules
#2: Chemical | ChemComp-EVM / | ||||||
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#3: Chemical | ChemComp-CA / | ||||||
#4: Chemical | ChemComp-NA / | ||||||
#5: Chemical | ChemComp-CL / | ||||||
#6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% PEG400, 100 mM calcium acetate, 100 mM Tris, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.17→50 Å / Num. obs: 22476 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Χ2: 0.9 / Net I/σ(I): 12.4 / Num. measured all: 252461 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JBQ Resolution: 2.17→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.122 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.167 / Details: PHENIX, PDB-REDO, REFMAC
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.04 Å2 / Biso mean: 31.347 Å2 / Biso min: 13.59 Å2
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Refinement step | Cycle: final / Resolution: 2.17→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.167→2.223 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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