+Open data
-Basic information
Entry | Database: PDB / ID: 4a1y | ||||||
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Title | Human myelin P2 protein, K65Q mutant | ||||||
Components | MYELIN P2 PROTEIN | ||||||
Keywords | TRANSPORT | ||||||
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: 1.2 Å | ||||||
Authors | Lehtimaki, M. / Kursula, P. | ||||||
Citation | Journal: To be Published Title: Structure-Function Relationships in the Myelin Peripheral Membrane Protein P2 Authors: Lehtimaki, M. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a1y.cif.gz | 278.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a1y.ent.gz | 229 KB | Display | PDB format |
PDBx/mmJSON format | 4a1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a1y_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4a1y_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4a1y_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 4a1y_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/4a1y ftp://data.pdbj.org/pub/pdb/validation_reports/a1/4a1y | HTTPS FTP |
-Related structure data
Related structure data | 4a1hC 4a8zC 2wutS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 14990.419 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTH27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P02689 #2: Chemical | ChemComp-PLM / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LYS 66 TO GLN ENGINEERED RESIDUE IN CHAIN B, LYS 66 TO GLN ...ENGINEERED | |
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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: 2.24 Å3/Da / Density % sol: 45.07 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.03317 | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2010 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.2→20 Å / Num. obs: 154219 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.5 | |||||||||||||||
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.4 / % possible all: 63.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WUT Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.508 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.008 / ESU R Free: 0.008 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.485 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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