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- PDB-7ntp: Human myelin P2 mutant V115A -

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Basic information

Entry
Database: PDB / ID: 7ntp
TitleHuman myelin P2 mutant V115A
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: 2.1 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 10, 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
B: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4404
Polymers29,9272
Non-polymers5132
Water82946
1
A: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2202
Polymers14,9631
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2202
Polymers14,9631
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.470, 91.220, 107.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-315-

HOH

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Components

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


Mass: 14963.417 Da / Num. of mol.: 2 / Mutation: V115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMP2 / 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.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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 / Density % sol: 64.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 2.2 M sodium malonate, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033222 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: 1.033222 Å / Relative weight: 1
ReflectionResolution: 2.1→42.732 Å / Num. obs: 24729 / % possible obs: 99.7 % / Redundancy: 4.93 % / Biso Wilson estimate: 58.98 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.078 / Net I/av σ(I): 11.15 / Net I/σ(I): 11.15
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.05 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1814 / CC1/2: 0.261 / % possible all: 99.9

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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: 2.1→42.73 Å / SU ML: 0.4103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.2387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2886 1237 5 %
Rwork0.237 23486 -
obs0.2396 24723 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 0 46 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592226
X-RAY DIFFRACTIONf_angle_d0.80842977
X-RAY DIFFRACTIONf_chiral_restr0.0636338
X-RAY DIFFRACTIONf_plane_restr0.0041372
X-RAY DIFFRACTIONf_dihedral_angle_d14.4712328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.42321350.40722568X-RAY DIFFRACTION99.93
2.18-2.280.41781370.36242594X-RAY DIFFRACTION99.74
2.28-2.40.42261350.34422569X-RAY DIFFRACTION99.93
2.4-2.550.38571360.3222583X-RAY DIFFRACTION99.96
2.55-2.750.35141370.30842598X-RAY DIFFRACTION99.82
2.75-3.030.33721360.29812596X-RAY DIFFRACTION99.89
3.03-3.470.33441380.25262612X-RAY DIFFRACTION99.82
3.47-4.370.25731390.21022632X-RAY DIFFRACTION99.64
4.37-42.730.23161440.18812734X-RAY DIFFRACTION98.97

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