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- PDB-6xvs: Human myelin protein P2 mutant P38G, unliganded -

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Basic information

Entry
Database: PDB / ID: 6xvs
TitleHuman myelin protein P2 mutant P38G, unliganded
ComponentsMyelin P2 proteinPMP2
KeywordsLIPID 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
Myelin P2 protein / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRuskamo, S. / Lehtimaki, M. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: 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
DepositionJan 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myelin P2 protein
B: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0273
Polymers29,9352
Non-polymers921
Water6,251347
1
A: Myelin P2 protein


Theoretical massNumber of molelcules
Total (without water)14,9671
Polymers14,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0602
Polymers14,9671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.540, 65.490, 82.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myelin P2 protein / PMP2 / Peripheral myelin protein 2


Mass: 14967.407 Da / Num. of mol.: 2 / Mutation: P38G
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 40% PEG 1000, 0.1 M citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.03 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 25915 / % possible obs: 91 % / Redundancy: 5.5 % / Biso Wilson estimate: 32 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.054 / Rsym value: 0.049 / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.85 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1211 / CC1/2: 0.77 / Rrim(I) all: 0.664 / Rsym value: 0.576 / % possible all: 58.4

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Processing

Software
NameVersionClassification
PHENIXdev_2247refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wut

2wut


Resolution: 1.8→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 -5 %random
Rwork0.1674 ---
obs0.1703 25864 91.1 %-
Displacement parametersBiso mean: 30.79 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 6 347 2445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172277
X-RAY DIFFRACTIONf_angle_d1.16713056
X-RAY DIFFRACTIONf_chiral_restr0.0633349
X-RAY DIFFRACTIONf_plane_restr0.0067385
X-RAY DIFFRACTIONf_dihedral_angle_d15.26061410

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