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Yorodumi- PDB-6mqw: Crystal Structure of All-trans Retinal-Bound R111K:Y134F:T54V:R13... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mqw | ||||||
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Title | Crystal Structure of All-trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E Human Cellular Retinoic Acid Binding Protein II Irradiated with 400 nm laser (30 seconds) and subsequently dark adapted (10 minutes) at 2.1 Angstrom Resolution | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | LIPID BINDING PROTEIN / iLBP / Rhodopsin mimic | ||||||
Function / homology | Function and homology information positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2019 Title: Mimicking Microbial Rhodopsin Isomerization in a Single Crystal. Authors: Ghanbarpour, A. / Nairat, M. / Nosrati, M. / Santos, E.M. / Vasileiou, C. / Dantus, M. / Borhan, B. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mqw.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mqw.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/6mqw ftp://data.pdbj.org/pub/pdb/validation_reports/mq/6mqw | HTTPS FTP |
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-Related structure data
Related structure data | 6mopC 6moqC 6morC 6movC 6moxC 6mpkC 6mqiC 6mqjC 6mqxC 6mqyC 6mqzC 6mr0C 4yfpS 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: 15594.747 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29373 |
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#2: Chemical | ChemComp-RET / |
#3: 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: 3.18 Å3/Da / Density % sol: 61.35 % / Description: hexagonal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, DL-malic acid / PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→35.645 Å / Num. obs: 12273 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.093 / Net I/σ(I): 36.75 |
Reflection shell | Resolution: 2.09→2.12 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1205 / Rrim(I) all: 0.754 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4yfp Resolution: 2.09→35.645 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.93 / Stereochemistry target values: ML
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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: 2.09→35.645 Å
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Refine LS restraints |
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LS refinement shell |
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