[English] 日本語
Yorodumi- PDB-3kv0: Crystal structure of HET-C2: A FUNGAL GLYCOLIPID TRANSFER PROTEIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kv0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of HET-C2: A FUNGAL GLYCOLIPID TRANSFER PROTEIN (GLTP) | ||||||
Components | HET-C2 | ||||||
Keywords | TRANSPORT PROTEIN / HET-C2 / GLTP / Glycolipid transfer protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Podospora anserina (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Simanshu, D.K. / Kenoth, R. / Brown, R.E. / Patel, D.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural determination and tryptophan fluorescence of heterokaryon incompatibility C2 protein (HET-C2), a fungal glycolipid transfer protein (GLTP), provide novel insights into glycolipid ...Title: Structural determination and tryptophan fluorescence of heterokaryon incompatibility C2 protein (HET-C2), a fungal glycolipid transfer protein (GLTP), provide novel insights into glycolipid specificity and membrane interaction by the GLTP fold. Authors: Kenoth, R. / Simanshu, D.K. / Kamlekar, R.K. / Pike, H.M. / Molotkovsky, J.G. / Benson, L.M. / Bergen, H.R. / Prendergast, F.G. / Malinina, L. / Venyaminov, S.Y. / Patel, D.J. / Brown, R.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kv0.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kv0.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kv0 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kv0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1swxS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23782.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Podospora anserina (fungus) / Gene: het-c2 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q01494 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris (pH 5.5-6.5) and 25 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 5.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2009 Details: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV. Vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry. |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 22551 / Redundancy: 8.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 36.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.95 / % possible all: 93.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: human apo-GLTP (PDB: 1SWX) Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.229 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.073 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|