+Open data
-Basic information
Entry | Database: PDB / ID: 7dei | ||||||
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Title | Structure of human ORP3 ORD domain in complex with PI(4)P | ||||||
Components | Oxysterol-binding protein-related protein 3 | ||||||
Keywords | TRANSPORT PROTEIN / phosphoinositide oxysterol-binding protein lipid transfer protein | ||||||
Function / homology | Function and homology information : / perinuclear endoplasmic reticulum / filopodium tip / bile acid biosynthetic process / cholesterol binding / Synthesis of bile acids and bile salts / nuclear membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / membrane ...: / perinuclear endoplasmic reticulum / filopodium tip / bile acid biosynthetic process / cholesterol binding / Synthesis of bile acids and bile salts / nuclear membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tong, J. / Tan, L. / Im, Y.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Plos One / Year: 2021 Title: Structure of human ORP3 ORD reveals conservation of a key function and ligand specificity in OSBP-related proteins. Authors: Tong, J. / Tan, L. / Im, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dei.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dei.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 7dei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7dei ftp://data.pdbj.org/pub/pdb/validation_reports/de/7dei | HTTPS FTP |
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-Related structure data
Related structure data | 7dejC 4inqS 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: 44940.535 Da / Num. of mol.: 2 / Mutation: C515S, C520S, deletion D859, D861G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL3, KIAA0704, ORP3, OSBP3 / Plasmid: pHis-GEX-4T / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H4L5 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.81 Å3/Da / Density % sol: 56.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES-NaOH pH 6.0, 25% PEG 1500, 0.1 M Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 31618 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 57.52 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 39 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1364 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4INQ Resolution: 2.6→46.45 Å / SU ML: 0.385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5013 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.45 Å
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Refine LS restraints |
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LS refinement shell |
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