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- PDB-6xu9: Human myelin protein P2 mutant K3N -

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Basic information

Entry
Database: PDB / ID: 6xu9
TitleHuman myelin protein P2 mutant K3N
ComponentsMyelin P2 protein
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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 17, 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

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Assembly

Deposited unit
A: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4604
Polymers14,9761
Non-polymers4843
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area7370 Å2
Unit cell
Length a, b, c (Å)64.520, 64.520, 101.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 14976.394 Da / Num. of mol.: 1 / Mutation: K3N
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 / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 35% PEG 6000, 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: 0.91 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 6311 / % possible obs: 99.5 % / Redundancy: 10.7 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.181 / Rsym value: 0.173 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 454 / CC1/2: 0.95 / Rrim(I) all: 0.838 / Rsym value: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev-2247refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wut

2wut


Resolution: 2.7→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 -5 %random
Rwork0.2124 ---
obs0.2143 6261 99.8 %-
Displacement parametersBiso mean: 36.37 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 32 39 1118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251097
X-RAY DIFFRACTIONf_angle_d0.51071465
X-RAY DIFFRACTIONf_chiral_restr0.0449166
X-RAY DIFFRACTIONf_plane_restr0.0017183
X-RAY DIFFRACTIONf_dihedral_angle_d18.2897678

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