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Yorodumi- PDB-4jgx: The Structure of Sterol Carrier Protein 2 from the Yeast Yarrowia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jgx | ||||||
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Title | The Structure of Sterol Carrier Protein 2 from the Yeast Yarrowia Lipolytica | ||||||
Components | Fatty acid-binding protein | ||||||
Keywords | LIPID BINDING PROTEIN / non specific lipid transfer / long chain fatty acids and CoA esters | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yarrowia lipolytica (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | De Berti, F.P. / Capaldi, S. / Acierno, J.P. / Klinke, S. / Monaco, H.L. / Ermacora, M.R. | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2013 Title: The crystal structure of sterol carrier protein 2 from Yarrowia lipolytica and the evolutionary conservation of a large, non-specific lipid-binding cavity. Authors: De Berti, F.P. / Capaldi, S. / Ferreyra, R. / Burgardt, N. / Acierno, J.P. / Klinke, S. / Monaco, H.L. / Ermacora, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jgx.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jgx.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jgx_validation.pdf.gz | 741.2 KB | Display | wwPDB validaton report |
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Full document | 4jgx_full_validation.pdf.gz | 745.7 KB | Display | |
Data in XML | 4jgx_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 4jgx_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jgx ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jgx | HTTPS FTP |
-Related structure data
Related structure data | 1iktS 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
#1: Protein | Mass: 14055.079 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Strain: CX-121-1B / Gene: SCP2, YALI0E01298g / Plasmid: pET9b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P80547 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 1.4M SODIUM CITRATE, 100MM HEPES, pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2011 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.19 Å / Num. all: 16154 / Num. obs: 16152 / % possible obs: 99.93 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.2→2.257 Å / Num. unique all: 989 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ikt Resolution: 2.2→29.19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.454 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.608 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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