+Open data
-Basic information
Entry | Database: PDB / ID: 6ew5 | ||||||
---|---|---|---|---|---|---|---|
Title | Human myelin protein P2 F57A mutant, monoclinic crystal form | ||||||
Components | Myelin P2 protein | ||||||
Keywords | LIPID TRANSPORT / fatty acid binding protein / beta barrel / portal region | ||||||
Function / homology | Function and homology information membrane organization / cholesterol binding / fatty acid transport / fatty acid binding / myelin sheath / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Laulumaa, S. / Lehtimaki, M. / Kursula, P. | ||||||
Citation | Journal: BMC Struct. Biol. / Year: 2018 Title: Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the beta barrel in fatty acid binding proteins. Authors: Laulumaa, S. / Nieminen, T. / Raasakka, A. / Krokengen, O.C. / Safaryan, A. / Hallin, E.I. / Brysbaert, G. / Lensink, M.F. / Ruskamo, S. / Vattulainen, I. / Kursula, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ew5.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ew5.ent.gz | 191.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ew5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ew5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ew5_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6ew5_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 6ew5_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/6ew5 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/6ew5 | HTTPS FTP |
-Related structure data
Related structure data | 6ew2C 6ew4C 2wutS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14915.374 Da / Num. of mol.: 4 / Mutation: F57A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PMP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02689 #2: Chemical | ChemComp-PLM / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.55 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 40-42% PEG 6000 / PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 40671 / % possible obs: 99.1 % / Redundancy: 6 % / CC1/2: 0.994 / Rrim(I) all: 0.173 / Rsym value: 0.158 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2958 / CC1/2: 0.754 / Rrim(I) all: 0.821 / Rsym value: 0.75 / % possible all: 98.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wut Resolution: 1.95→19.49 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.77
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→19.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|