+Open data
-Basic information
Entry | Database: PDB / ID: 2r55 | ||||||
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Title | Human StAR-related lipid transfer protein 5 | ||||||
Components | StAR-related lipid transfer protein 5 | ||||||
Keywords | TRANSPORT PROTEIN / alpha and beta protein / cholesterol binding / Structural Genomics / Structural Genomics Consortium / SGC / Lipid transport / Lipid-binding / Transport | ||||||
Function / homology | Function and homology information cholesterol import / cholesterol transfer activity / bile acid and bile salt transport / bile acid binding / cholesterol binding / Recycling of bile acids and salts / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Lehtio, L. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Herman, M.D. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Persson, C. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Comparative structural analysis of lipid binding START domains. Authors: Thorsell, A.G. / Lee, W.H. / Persson, C. / Siponen, M.I. / Nilsson, M. / Busam, R.D. / Kotenyova, T. / Schuler, H. / Lehtio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r55.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r55.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/2r55 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/2r55 | HTTPS FTP |
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-Related structure data
Related structure data | 2psoC 3fo5C 3p0lC 1jssS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 2 - 213 / Label seq-ID: 20 - 231
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Details | Authors state that each chain represents a biological monomer. |
-Components
#1: Protein | Mass: 25983.459 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STARD5 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NSY2 #2: 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: 2.36 Å3/Da / Density % sol: 47.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG 6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.03992 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111), Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03992 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 16487 / Num. obs: 16487 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.4 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.25 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 5.94 / Num. unique all: 1840 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JSS Resolution: 2.5→19.99 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 30.63 / SU ML: 0.322 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.943 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 68.472 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.99 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1646 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.564 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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