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Yorodumi- PDB-6vid: The Crystal Structure of Aps Domain-Swapped Trimer Q108K:K40D:T53... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vid | ||||||
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Title | The Crystal Structure of Aps Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Variant of HCRBPII | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | LIPID BINDING PROTEIN / Domain Swapped Trimer / iLBP | ||||||
Function / homology | Function and homology information vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of Apo Domain Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F variant of HCRBPII 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 | 6vid.cif.gz | 202.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vid.ent.gz | 131.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vid_validation.pdf.gz | 279.3 KB | Display | wwPDB validaton report |
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Full document | 6vid_full_validation.pdf.gz | 279.5 KB | Display | |
Data in XML | 6vid_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 6vid_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/6vid ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6vid | HTTPS FTP |
-Related structure data
Related structure data | 2rcqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 3 - 132 / Label seq-ID: 3 - 132
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-Components
#1: Protein | Mass: 15548.438 Da / Num. of mol.: 6 / Mutation: Q108K, K40D, T53A, R58L, Q38F, Q4F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Bacterial expression vector pAIL2 (others) / References: UniProt: P50120 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.16 Å3/Da / Density % sol: 43.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Sodium acetate, Ammonium acetate |
-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: Feb 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.891→49.282 Å / Num. obs: 18585 / % possible obs: 99.43 % / Redundancy: 7.7 % / Biso Wilson estimate: 61.48 Å2 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.047 / Rrim(I) all: 0.178 / Net I/av σ(I): 22.88 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 2.891→2.994 Å / Rmerge(I) obs: 0.115 / Num. unique obs: 1745 / CC1/2: 0.804 / Rrim(I) all: 1.316 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RCQ Resolution: 2.89→49.28 Å / SU ML: 0.3762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1766 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→49.28 Å
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Refine LS restraints |
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LS refinement shell |
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