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- PDB-7nrw: Human myelin protein P2 mutant M114T -

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Basic information

Entry
Database: PDB / ID: 7nrw
TitleHuman myelin protein P2 mutant M114T
ComponentsMyelin P2 protein
KeywordsLIPID BINDING PROTEIN / myelin / fatty-acid binding protein / Charcot-Marie-Tooth disease
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: 2 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 4, 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)15,3025
Polymers14,9611
Non-polymers3404
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-21 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.790, 64.790, 100.930
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: 14961.378 Da / Num. of mol.: 1 / Mutation: M114T
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-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.57 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Sodium malonate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 15156 / % possible obs: 99.9 % / Redundancy: 13.8 % / Biso Wilson estimate: 37.24 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.255 / Net I/σ(I): 11.59
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1092 / CC1/2: 0.703 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BVM

4bvm


Resolution: 2→41.72 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2499 --
Rwork0.207 --
obs-15042 99.57 %
Displacement parametersBiso mean: 44.91 Å2
Refinement stepCycle: LAST / Resolution: 2→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 3 69 1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01231097
X-RAY DIFFRACTIONf_angle_d1.11771464
X-RAY DIFFRACTIONf_chiral_restr0.0567168
X-RAY DIFFRACTIONf_plane_restr0.006181
X-RAY DIFFRACTIONf_dihedral_angle_d19.2029435

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