+Open data
-Basic information
Entry | Database: PDB / ID: 6xvq | ||||||
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Title | Human myelin protein P2 mutant K31Q | ||||||
Components | Myelin P2 protein | ||||||
Keywords | LIPID BINDING PROTEIN / mutant / peripheral membrane protein / FABP / beta barrel | ||||||
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: 1.8 Å | ||||||
Authors | Ruskamo, S. / Lehtimaki, M. / Kursula, P. | ||||||
Funding support | Finland, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Cryo-EM, X-ray diffraction, and atomistic simulations reveal determinants for the formation of a supramolecular myelin-like proteolipid lattice. Authors: Ruskamo, S. / Krokengen, O.C. / Kowal, J. / Nieminen, T. / Lehtimaki, M. / Raasakka, A. / Dandey, V.P. / Vattulainen, I. / Stahlberg, H. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xvq.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xvq.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xvq_validation.pdf.gz | 676 KB | Display | wwPDB validaton report |
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Full document | 6xvq_full_validation.pdf.gz | 677 KB | Display | |
Data in XML | 6xvq_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 6xvq_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/6xvq ftp://data.pdbj.org/pub/pdb/validation_reports/xv/6xvq | HTTPS FTP |
-Related structure data
Related structure data | 6stsC 6xu5C 6xu9C 6xuaC 6xuwC 6xvrC 6xvsC 6xvyC 6xw9C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14990.419 Da / Num. of mol.: 1 / Mutation: K31Q 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 |
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#2: Chemical | ChemComp-PLM / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 32% PEG 6000, 0.1 M citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.91 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 16817 / % possible obs: 98.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.117 / Rsym value: 0.111 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1217 / CC1/2: 0.78 / Rrim(I) all: 0.981 / Rsym value: 0.926 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wut Resolution: 1.8→40 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 18.05 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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Refine LS restraints |
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