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- PDB-5n4m: Human myelin protein P2, mutant I43N -

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Basic information

Entry
Database: PDB / ID: 5n4m
TitleHuman myelin protein P2, mutant I43N
ComponentsMyelin P2 protein
KeywordsLIPID BINDING PROTEIN / fatty acid 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 / 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
D-MALATE / PALMITIC ACID / VACCENIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRuskamo, S. / Kursula, P.
CitationJournal: Sci Rep / Year: 2017
Title: Molecular mechanisms of Charcot-Marie-Tooth neuropathy linked to mutations in human myelin protein P2.
Authors: Ruskamo, S. / Nieminen, T. / Kristiansen, C.K. / Vatne, G.H. / Baumann, A. / Hallin, E.I. / Raasakka, A. / Joensuu, P. / Bergmann, U. / Vattulainen, I. / Kursula, P.
History
DepositionFeb 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6654
Polymers14,9921
Non-polymers6733
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint8 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.997, 64.997, 101.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 14992.415 Da / Num. of mol.: 1
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-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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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: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.1 M DL-malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→45.96 Å / Num. obs: 29518 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.17 Å2 / CC1/2: 1 / Rrim(I) all: 0.07 / Rsym value: 0.067 / Net I/σ(I): 18.4
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.7 / Num. unique all: 2710 / CC1/2: 0.734 / Rrim(I) all: 3.27 / Rsym value: 3 / % possible all: 89.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BVM

4bvm


Resolution: 1.59→45.96 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.55
RfactorNum. reflection% reflection
Rfree0.2136 1990 6.77 %
Rwork0.1837 --
obs0.1857 29399 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 202.15 Å2 / Biso mean: 43.797 Å2 / Biso min: 23.52 Å2
Refinement stepCycle: final / Resolution: 1.59→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 115 134 1296
Biso mean--53.7 44.62 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071204
X-RAY DIFFRACTIONf_angle_d1.0131616
X-RAY DIFFRACTIONf_chiral_restr0.04180
X-RAY DIFFRACTIONf_plane_restr0.004205
X-RAY DIFFRACTIONf_dihedral_angle_d13.231499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.59-1.62980.45621190.47691633175284
1.6298-1.67390.36781400.38481927206799
1.6739-1.72310.34181400.33221917205799
1.7231-1.77870.33231420.260519402082100
1.7787-1.84230.28191410.2391951209299
1.8423-1.91610.27831390.24941957209699
1.9161-2.00330.30511420.23021946208899
2.0033-2.10890.23651440.20419782122100
2.1089-2.2410.24391440.187719722116100
2.241-2.4140.18451440.195219762120100
2.414-2.6570.19471430.201619762119100
2.657-3.04140.24361460.197420192165100
3.0414-3.83150.19451480.162720502198100
3.8315-45.9790.1721580.140321672325100

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