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Yorodumi- PDB-3pc3: Full length structure of cystathionine beta-synthase from Drosoph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pc3 | ||||||
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Title | Full length structure of cystathionine beta-synthase from Drosophila in complex with aminoacrylate | ||||||
Components | CG1753, isoform A | ||||||
Keywords | LYASE / CBS / synthase / PLP / Heme / Aminoacrylate | ||||||
Function / homology | Function and homology information Cysteine formation from homocysteine / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / homocysteine metabolic process / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / nitrite reductase (NO-forming) activity / response to endoplasmic reticulum stress ...Cysteine formation from homocysteine / cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / homocysteine metabolic process / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / nitrite reductase (NO-forming) activity / response to endoplasmic reticulum stress / determination of adult lifespan / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.55 Å | ||||||
Authors | Koutmos, M. / Smith, J.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine {beta}-synthase. Authors: Koutmos, M. / Kabil, O. / Smith, J.L. / Banerjee, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pc3.cif.gz | 238.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pc3.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/3pc3 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/3pc3 | HTTPS FTP |
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-Related structure data
Related structure data | 3pc2SC 3pc4C S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 57469.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG1753, Dmel_CG1753 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9VRD9, cystathionine beta-synthase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-P1T / |
#4: 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: 2.11 Å3/Da / Density % sol: 41.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 23% PEG 3350, 0.2 Li2SO4, 100 mM BIS-TRIS 6.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2010 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. all: 70759 / Num. obs: 66372 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Χ2: 0.945 / Net I/σ(I): 11.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: PHASER Starting model: PDB entry 3PC2 Resolution: 1.55→41.45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2038 / WRfactor Rwork: 0.1602 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9048 / SU B: 2.725 / SU ML: 0.045 / SU R Cruickshank DPI: 0.113 / SU Rfree: 0.0827 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.63 Å2 / Biso mean: 17.7789 Å2 / Biso min: 5.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→41.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.591 Å / Total num. of bins used: 20
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