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- PDB-7nsr: Myelin protein P2 I50del -

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Basic information

Entry
Database: PDB / ID: 7nsr
TitleMyelin protein P2 I50del
ComponentsMyelin P2 protein
KeywordsLIPID BINDING PROTEIN / Membrane binding protein
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
Similarity search - Domain/homology
PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUusitalo, M. / Ruskamo, S. / Kursula, P.
CitationJournal: Febs J. / Year: 2021
Title: Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants.
Authors: Uusitalo, M. / Klenow, M.B. / Laulumaa, S. / Blakeley, M.P. / Simonsen, A.C. / Ruskamo, S. / Kursula, P.
History
DepositionMar 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)15,2195
Polymers14,8781
Non-polymers3404
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-17 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.140, 66.140, 101.190
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: 14878.313 Da / Num. of mol.: 1 / Mutation: I50del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMP2 / Plasmid: pTH27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P02689
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.49 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 1.9 M Sodium malonate dibasic monohydrate pH 6.4

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→46.77 Å / Num. obs: 36689 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 26.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.64
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 13.69 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2657 / CC1/2: 0.743 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NR3

3nr3


Resolution: 1.5→46.77 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1986 1829 5 %
Rwork0.1818 34756 -
obs0.1827 36585 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 21 137 1198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02151215
X-RAY DIFFRACTIONf_angle_d1.88041634
X-RAY DIFFRACTIONf_chiral_restr0.1297180
X-RAY DIFFRACTIONf_plane_restr0.0117209
X-RAY DIFFRACTIONf_dihedral_angle_d11.0557201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.43071380.37052606X-RAY DIFFRACTION99.17
1.54-1.590.33251380.31522614X-RAY DIFFRACTION99.28
1.59-1.640.30651370.27632621X-RAY DIFFRACTION99.67
1.64-1.70.23451380.23872630X-RAY DIFFRACTION99.53
1.7-1.760.22641370.21432614X-RAY DIFFRACTION99.49
1.76-1.840.25711390.20312645X-RAY DIFFRACTION99.78
1.84-1.940.21861410.18842661X-RAY DIFFRACTION99.82
1.94-2.060.21611400.1772651X-RAY DIFFRACTION99.79
2.06-2.220.17321390.16852669X-RAY DIFFRACTION99.86
2.22-2.450.20381420.16832695X-RAY DIFFRACTION100
2.45-2.80.18771420.1912702X-RAY DIFFRACTION99.96
2.8-3.530.21681450.19072744X-RAY DIFFRACTION100
3.53-46.770.1661530.1572904X-RAY DIFFRACTION99.97

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