[English] 日本語
Yorodumi- PDB-4zh9: Crystal Structure of the Domain-Swapped Dimer Wild-Type of Human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zh9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Domain-Swapped Dimer Wild-Type of Human Cellular Retinol Binding Protein II | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / Domain Swapped Dimer / Domain Swapping / Protein folding / Human Cellular Retinol Binding Protein II / Intra Cellular Retinol Binding Protein II | ||||||
Function / homology | Function and homology information vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / fatty acid transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | ||||||
Authors | Assar, Z. / Nossoni, Z. / Geiger, J.H. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Structure / Year: 2016 Title: Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates. Authors: Assar, Z. / Nossoni, Z. / Wang, W. / Santos, E.M. / Kramer, K. / McCornack, C. / Vasileiou, C. / Borhan, B. / Geiger, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of holo wild-type human cellular retinol-binding protein II (hCRBPII) bound to retinol and retinal. Authors: Nossoni, Z. / Assar, Z. / Yapici, I. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J. #2: Journal: Science / Year: 2012 Title: Tuning the electronic absorption of protein-embedded all-trans-retinal. Authors: Wang, W. / Nossoni, Z. / Berbasova, T. / Watson, C.T. / Yapici, I. / Lee, K.S. / Vasileiou, C. / Geiger, J.H. / Borhan, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zh9.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zh9.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 4zh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zh9_validation.pdf.gz | 420.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4zh9_full_validation.pdf.gz | 421.9 KB | Display | |
Data in XML | 4zh9_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 4zh9_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/4zh9 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zh9 | HTTPS FTP |
-Related structure data
Related structure data | 4zcbC 4zguC 4zh6C 4zj0C 4zr2C 5dg4C 5dpqC 2rctS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | Dimer confirmed by gel filtration |
-Components
#1: Protein | Mass: 15597.452 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: P50120 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.28 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG 4000 (40%), 0.1M Sodium Acetate pH 4.5, Ammonium Acetate 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→50 Å / Num. obs: 4455 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 2.41 |
Reflection shell | Resolution: 2.66→3.04 Å / Rmerge(I) obs: 0.731 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RCT Resolution: 2.66→43.989 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 25.06 / Stereochemistry target values: LS_WUNIT_K1
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.66→43.989 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 2.7298 Å / Origin y: 36.4241 Å / Origin z: -2.9222 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |