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Yorodumi- PDB-6z2z: M2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z2z | ||||||
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Title | M2 mutant (R111K:Y134F:T54V:R132Q:P39Y:R59Y) of human cellular retinoic acid binding protein II - 2a conjugate | ||||||
Components | Cellular retinoic acid-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / human cellular retinoic acid binding protein II / hCRABPII / conjugate / chromophore / M2 | ||||||
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 / signal transduction / endoplasmic reticulum / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Tassone, G. / Pozzi, C. / Mangani, S. | ||||||
Citation | Journal: Chembiochem / Year: 2022 Title: Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein. Authors: Tassone, G. / Paolino, M. / Pozzi, C. / Reale, A. / Salvini, L. / Giorgi, G. / Orlandini, M. / Galvagni, F. / Mangani, S. / Yang, X. / Carlotti, B. / Ortica, F. / Latterini, L. / Olivucci, M. / Cappelli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z2z.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z2z.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 6z2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z2z_validation.pdf.gz | 734 KB | Display | wwPDB validaton report |
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Full document | 6z2z_full_validation.pdf.gz | 736.1 KB | Display | |
Data in XML | 6z2z_validation.xml.gz | 8 KB | Display | |
Data in CIF | 6z2z_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/6z2z ftp://data.pdbj.org/pub/pdb/validation_reports/z2/6z2z | HTTPS FTP |
-Related structure data
Related structure data | 6z2uC 6zswC 6zsxC 4yfpS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 15992.265 Da / Num. of mol.: 1 / Mutation: R111K, Y134F, T54V, R132Q, P39Y, R59Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRABP2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29373 |
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#2: Chemical | ChemComp-Q5W / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 61.36 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium malonate pH 7 and 20% w/v polyethylene glycol 3,350 PH range: 6.0-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 3, 2019 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→101.15 Å / Num. obs: 6999 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.064 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 986 / CC1/2: 0.948 / Rpim(I) all: 0.17 / Rrim(I) all: 0.485 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YFP Resolution: 2.55→50.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.677 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98 Å2 / Biso mean: 64.37 Å2 / Biso min: 39.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3404 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→50.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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