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- PDB-5n4q: Human myelin protein P2, mutant T51P -

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Basic information

Entry
Database: PDB / ID: 5n4q
TitleHuman myelin protein P2, mutant T51P
ComponentsMyelin P2 proteinPMP2
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: 1.72 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

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Assembly

Deposited unit
A: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6604
Polymers14,9871
Non-polymers6733
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint8 kcal/mol
Surface area7100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.024, 66.024, 100.859
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 / PMP2 / Peripheral myelin protein 2


Mass: 14987.481 Da / Num. of mol.: 1 / Mutation: T51P
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 / 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 / Vaccenic 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 / Malic acid


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.67 Å3/Da / Density % sol: 66.46 %
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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.72→46.686 Å / Num. obs: 44944 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.081 / Rsym value: 0.074 / Net I/σ(I): 12.4
Reflection shellResolution: 1.72→1.87 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.8 / Num. unique all: 7154 / CC1/2: 0.678 / Rrim(I) all: 2.92 / Rsym value: 2.67 / % possible all: 97.5

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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: 1.72→46.686 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.49
RfactorNum. reflection% reflection
Rfree0.191 1841 7.56 %
Rwork0.1668 --
obs0.1686 24342 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.71 Å2 / Biso mean: 39.7015 Å2 / Biso min: 22.83 Å2
Refinement stepCycle: final / Resolution: 1.72→46.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 115 139 1301
Biso mean--44.72 42.7 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061260
X-RAY DIFFRACTIONf_angle_d0.9741689
X-RAY DIFFRACTIONf_chiral_restr0.036184
X-RAY DIFFRACTIONf_plane_restr0.005217
X-RAY DIFFRACTIONf_dihedral_angle_d14.185522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.76650.48351380.4481669180799
1.7665-1.81850.39611360.35411679181599
1.8185-1.87720.28031380.271817081846100
1.8772-1.94430.2661400.226117171857100
1.9443-2.02220.27331390.21316891828100
2.0222-2.11420.2281400.16917061846100
2.1142-2.22570.20251410.157117151856100
2.2257-2.36510.16681410.154817331874100
2.3651-2.54770.1761420.155417271869100
2.5477-2.80410.22121410.17317341875100
2.8041-3.20970.2071430.170817421885100
3.2097-4.04360.15621470.140317901937100
4.0436-46.70320.1541550.149418922047100

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