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Yorodumi- PDB-6c2h: Crystal Structures of Cystathionine beta-Synthase from Saccharomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c2h | ||||||
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Title | Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the Catalytic Core | ||||||
Components | Cystathionine beta-synthaseCystathionine beta synthase | ||||||
Keywords | LYASE / CBS / synthase / PLP | ||||||
Function / homology | Function and homology information Cysteine formation from homocysteine / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / 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 / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / 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: 1.49 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 | 6c2h.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c2h.ent.gz | 136.8 KB | Display | PDB format |
PDBx/mmJSON format | 6c2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/6c2h ftp://data.pdbj.org/pub/pdb/validation_reports/c2/6c2h | HTTPS FTP |
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-Related structure data
Related structure data | 6c2qC 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
-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) (bacteria) / References: UniProt: P32582, cystathionine beta-synthase |
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-Non-polymers , 9 types, 354 molecules
#2: Chemical | ChemComp-PLP / | ||||||
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#3: Chemical | ChemComp-ACT / | ||||||
#4: Chemical | ChemComp-CA / | ||||||
#5: Chemical | ChemComp-NA / | ||||||
#6: Chemical | ChemComp-CL / | ||||||
#7: Chemical | #8: Chemical | ChemComp-PGE / | #9: Chemical | #10: 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: 2.62 Å3/Da / Density % sol: 53.11 % |
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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: 1.49→50 Å / Num. obs: 66342 / % possible obs: 99 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.033 / Rrim(I) all: 0.109 / Χ2: 0.88 / Net I/σ(I): 6.2 / Num. measured all: 706797 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.49→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.141 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.057 / Details: PHENIX, PDB-REDO, REFMAC
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.45 Å2 / Biso mean: 18.747 Å2 / Biso min: 7.19 Å2
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Refinement step | Cycle: final / Resolution: 1.49→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.493→1.532 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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