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Yorodumi- PDB-6c4p: Crystal Structures of Cystathionine beta-Synthase from Saccharomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c4p | ||||||
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Title | Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PMP Complex | ||||||
Components | Cystathionine 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: 2.3 Å | ||||||
Authors | Kreinbring, C.A. / Tu, Y. / Liu, D. / Berkowitz, D.B. / 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 | 6c4p.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c4p.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 6c4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c4p_validation.pdf.gz | 784.9 KB | Display | wwPDB validaton report |
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Full document | 6c4p_full_validation.pdf.gz | 784.9 KB | Display | |
Data in XML | 6c4p_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 6c4p_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/6c4p ftp://data.pdbj.org/pub/pdb/validation_reports/c4/6c4p | HTTPS FTP |
-Related structure data
Related structure data | 6c2hC 6c2qC 6c2zC 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 Details: catalytic core 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 , 7 types, 95 molecules
#2: Chemical | ChemComp-PMP / | ||||
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#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | ChemComp-NA / | ||||
#5: Chemical | ChemComp-CL / | ||||
#6: Chemical | #7: Chemical | #8: 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: 2.58 Å3/Da / Density % sol: 52.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, pH 8.0, 30% PEG400, 100 mM calcium acetate |
-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: 2.3→50 Å / Num. obs: 17876 / % possible obs: 96 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.03 / Rrim(I) all: 0.091 / Χ2: 0.98 / Net I/σ(I): 17 / Num. measured all: 113960 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.3→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.083 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.215 / 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 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.2 Å2 / Biso mean: 46.396 Å2 / Biso min: 24.78 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.304→2.364 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.239 Å / Origin y: 30.573 Å / Origin z: -12.663 Å
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