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Yorodumi- PDB-7ry5: Cellular Retinoic Acid Binding Protein II with Bound Inhibitor 4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ry5 | ||||||
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Title | Cellular Retinoic Acid Binding Protein II with Bound Inhibitor 4-[6-({4-[(fluorosulfonyl)oxy]phenyl}ethynyl)-4,4-dimethyl-3,4-dihydroquinolin-1(2H)-yl]-4-oxobutanoic acid | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / Inhibitor complex / SIGNALING PROTEIN-INHIBITOR complex | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kimmel, B.R. / Mrksich, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemistry / Year: 2021 Title: Development of an Enzyme-Inhibitor Reaction Using Cellular Retinoic Acid Binding Protein II for One-Pot Megamolecule Assembly. Authors: Kimmel, B.R. / Mrksich, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ry5.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ry5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ry5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ry5_validation.pdf.gz | 855.1 KB | Display | wwPDB validaton report |
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Full document | 7ry5_full_validation.pdf.gz | 856.1 KB | Display | |
Data in XML | 7ry5_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 7ry5_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/7ry5 ftp://data.pdbj.org/pub/pdb/validation_reports/ry/7ry5 | HTTPS FTP |
-Related structure data
Related structure data | 6hkrS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.2210/image_data.cif / Data set type: diffraction image 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: 17393.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P29373 #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: 2.21 Å3/Da / Density % sol: 44.24 % Description: Long thin needles growing in clusters, which had to be mechanically separated for data collection. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Sodium Acetate, 18% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 17, 2021 |
Radiation | Monochromator: C(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 21965 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Χ2: 1.621 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.57 / Num. unique obs: 2169 / CC1/2: 0.877 / CC star: 0.967 / Rpim(I) all: 0.236 / Rrim(I) all: 0.602 / Χ2: 0.964 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6HKR Resolution: 2→35.057 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.159 / SU B: 4.204 / SU ML: 0.115 / Average fsc free: 0.9252 / Average fsc work: 0.9411 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.168 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: 24.819 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.057 Å
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Refine LS restraints |
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LS refinement shell |
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