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Yorodumi- PDB-6noe: Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6noe | ||||||
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Title | Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E:I63D Mutant of Human Cellular Retinoic Acid Binding Protein II in the Dark at 1.97 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å | ||||||
Authors | Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the All-Trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E:I63D Mutant of Human Cellular Retinoic Acid Binding Protein II in the Dark at 1.97 Angstrom Resolution Authors: Ghanbarpour, A. / Geiger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6noe.cif.gz | 43.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6noe.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 6noe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6noe_validation.pdf.gz | 627.3 KB | Display | wwPDB validaton report |
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Full document | 6noe_full_validation.pdf.gz | 628.6 KB | Display | |
Data in XML | 6noe_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 6noe_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6noe ftp://data.pdbj.org/pub/pdb/validation_reports/no/6noe | HTTPS FTP |
-Related structure data
Related structure data | 4yfpS S: Starting model for refinement |
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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: 15596.677 Da / Num. of mol.: 1 Mutation: R111K, Y134F, T54V, R132Q, P39Y, R59Y, L121E, I63D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.94 % / Description: Hexagonal |
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Crystal grow | Temperature: 277 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.969→35.74 Å / Num. obs: 13837 / % possible obs: 93.06 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.969→2.04 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1398 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YFP Resolution: 1.969→35.738 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.57 / 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: 1.969→35.738 Å
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Refine LS restraints |
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LS refinement shell |
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