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- PDB-7o60: Crystal structure of human myelin protein P2 at room temperature ... -

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Basic information

Entry
Database: PDB / ID: 7o60
TitleCrystal structure of human myelin protein P2 at room temperature from joint X-ray and neutron refinement.
ComponentsMyelin P2 protein
KeywordsLIPID BINDING PROTEIN / myelin / fatty acid binding protein / neuropathy / beta barrel
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
CITRIC ACID / DEUTERATED WATER / PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLaulumaa, S. / Blakeley, M.P. / 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
DepositionApr 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 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 1.3May 1, 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)15,4403
Polymers14,9911
Non-polymers4492
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint4 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.952, 57.952, 100.790
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: 14991.470 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: D2O
Has ligand of interestN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: 28% PEG 6000, 0.1 M citrate, pD 4.75

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12921N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORILL LADI III13.0-3.9
SEALED TUBEXenocs GeniX 3D Cu HF21.54
Detector
TypeIDDetectorDate
LADI III1AREA DETECTORSep 2, 2014
MAR scanner 345 mm plate2IMAGE PLATEMay 2, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
131
23.91
31.541
Reflection

Biso Wilson estimate: 27.66 Å2 / Entry-ID: 7O60

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rrim(I) allRsym valueDiffraction-IDNet I/σ(I)
2-151246498.99.70.9990.0630.06225.2
2.4-40423260.14.20.18916.1
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allRsym valueDiffraction-ID% possible all
2-2.063.238910.8490.5130.431296.1
2.4-2.532.22.83630.304136.9

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Processing

Software
NameVersionClassification
PHENIXdev_3928refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Refinement

SU ML: 0.167 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 19.3163 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 2WUT

2wut

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
2-14.53X-RAY DIFFRACTION18.850.20320.15460.15961246111971244310.0198.9721.34
2.4-40NEUTRON DIFFRACTION0.34120.29470.299542271058.91
Refinement stepCycle: LAST / Resolution: 2→14.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 31 105 1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02921104
X-RAY DIFFRACTIONf_angle_d2.08521474
X-RAY DIFFRACTIONf_chiral_restr0.104167
X-RAY DIFFRACTIONf_plane_restr0.0129203
X-RAY DIFFRACTIONf_dihedral_angle_d17.656440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.060.2391300.19051169X-RAY DIFFRACTION95.1
2.06-2.150.22721360.17541216X-RAY DIFFRACTION99.27
2.15-2.260.24081360.16561222X-RAY DIFFRACTION99.93
2.26-2.40.21411370.17261240X-RAY DIFFRACTION99.93
2.4-2.590.23251370.16591235X-RAY DIFFRACTION100
2.59-2.850.23191380.17051247X-RAY DIFFRACTION100
2.85-3.260.23341420.17191264X-RAY DIFFRACTION100
3.26-4.090.19291410.13621284X-RAY DIFFRACTION99.93
4.09-14.530.15841490.13441320X-RAY DIFFRACTION96.77

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