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Yorodumi- PDB-4gqv: Crystal structure of CBS-pair protein, CBSX1 from Arabidopsis thaliana -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gqv | ||||||
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Title | Crystal structure of CBS-pair protein, CBSX1 from Arabidopsis thaliana | ||||||
Components | CBS domain-containing protein CBSX1, chloroplastic | ||||||
Keywords | PROTEIN BINDING / CBS domain / Thioredoxin / Chloroplast / plant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 Å | ||||||
Authors | Jeong, B.-C. / Park, S.H. / Yoo, K.S. / Shin, J.S. / Song, H.K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: Crystal structure of the single cystathionine beta-synthase domain-containing protein CBSX1 from Arabidopsis thaliana Authors: Jeong, B.C. / Park, S.H. / Yoo, K.S. / Shin, J.S. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gqv.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gqv.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 4gqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/4gqv ftp://data.pdbj.org/pub/pdb/validation_reports/gq/4gqv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18226.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AP22.61, At4g36910, C7A10.450, CBSX1, CDCP2 / Plasmid: pET-GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O23193 |
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#2: 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: 2.08 Å3/Da / Density % sol: 40.8 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 100mM phophate-acetate pH 4.2, 200mM NaCl, 20%(w/w) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2007 |
Radiation | Monochromator: Double-crystal Si(111) liquid-nitrogen-cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.392→50 Å / Num. obs: 11556 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.1 % / Biso Wilson estimate: 60.27 Å2 / Rsym value: 0.069 / Net I/σ(I): 60.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.392→31.527 Å / SU ML: 0.4 / σ(F): 1.36 / Phase error: 32.78 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.392→31.527 Å
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Refine LS restraints |
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LS refinement shell |
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