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- PDB-6nnx: Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nnx | ||||||
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Title | Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121M Mutant of Human Cellular Retinoic Acid Binding Protein II in the Dark at 1.87 Angstrom Resolution | ||||||
![]() | Cellular retinoic acid-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / iLBP / Rhodopsin mimic | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121M Mutant of Human Cellular Retionic Acid Binding Protein II in the Dark at 1.87 Angstrom Resolution Authors: Ghanbarpour, A. / Geiger, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.6 KB | Display | ![]() |
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PDB format | ![]() | 29.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 622.7 KB | Display | ![]() |
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Full document | ![]() | 623.4 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yfpS S: Starting model for refinement |
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Similar structure data |
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Links
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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: 15596.829 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pBEN1-SGC (others) References: UniProt: P29373 |
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#2: Chemical | ChemComp-RET / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.43 % / Description: Hexagonal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium Malonate / PH range: 6-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→45.36 Å / Num. obs: 16795 / % possible obs: 98.33 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.87→1.937 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1647 / % possible all: 98.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YFP Resolution: 1.87→45.36 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→45.36 Å
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Refine LS restraints |
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LS refinement shell |
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