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- PDB-7a9y: Structural comparison of cellular retinoic acid binding protein I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a9y | ||||||
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Title | Structural comparison of cellular retinoic acid binding protein I and II in the presence and absence of natural and synthetic ligands | ||||||
![]() | Cellular retinoic acid-binding protein 1 | ||||||
![]() | SIGNALING PROTEIN / Retinoic Acid / Retinoid / CRABP | ||||||
Function / homology | ![]() retinoic acid catabolic process / RA biosynthesis pathway / retinoid binding / retinal binding / retinoic acid binding / retinol binding / fatty acid transport / fatty acid binding / signal transduction / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomlinson, C.W.E. / Cornish, K.A.S. / Pohl, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-functional relationship of cellular retinoic acid-binding proteins I and II interacting with natural and synthetic ligands. Authors: Tomlinson, C.W.E. / Cornish, K.A.S. / Whiting, A. / Pohl, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 458.6 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a9zC ![]() 7aa0C ![]() 7aa1C ![]() 1cbrS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 136 / Label seq-ID: 2 - 136
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
#1: Protein | Mass: 15575.536 Da / Num. of mol.: 2 / Mutation: L29C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MYR / | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-TDA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG mixture |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→36.05 Å / Num. obs: 43110 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.029 / Rrim(I) all: 0.029 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.791 / Num. unique obs: 4050 / CC1/2: 0.48 / Rpim(I) all: 0.559 / Rrim(I) all: 0.559 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CBR Resolution: 1.64→36.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.249 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.088 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.424 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→36.05 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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