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- PDB-4d6b: Human myelin protein P2, mutant P38G -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4d6b
TitleHuman myelin protein P2, mutant P38G
ComponentsMYELIN P2 PROTEIN
KeywordsSTRUCTURAL 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
PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.116 Å
AuthorsLaulumaa, S. / Lehtimaki, M. / Kursula, P.
CitationJournal: Plos One / Year: 2015
Title: Dynamics of the Peripheral Membrane Protein P2 from Human Myelin Measured by Neutron Scattering-A Comparison between Wild-Type Protein and a Hinge Mutant.
Authors: Laulumaa, S. / Nieminen, T. / Lehtimaki, M. / Aggarwal, S. / Simons, M. / Koza, M.M. / Vattulainen, I. / Kursula, P. / Natali, F.
History
DepositionNov 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)15,7848
Polymers14,9511
Non-polymers8337
Water73941
1
A: MYELIN P2 PROTEIN
hetero molecules

A: MYELIN P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,56816
Polymers29,9032
Non-polymers1,66614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4470 Å2
ΔGint-120.7 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.311, 64.311, 101.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MYELIN P2 PROTEIN / PERIPHERAL MYELIN PROTEIN 2 / MYELIN PROTEIN P2


Mass: 14951.407 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTH27 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02689
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.5 Å3/Da / Density % sol: 64.91 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.12→20 Å / Num. obs: 12434 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 43.99 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.5
Reflection shellResolution: 2.12→2.17 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.7 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUT

2wut


Resolution: 2.116→19.335 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 35.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 620 5 %
Rwork0.2185 --
obs0.2211 12409 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.116→19.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 48 41 1134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041105
X-RAY DIFFRACTIONf_angle_d0.6671476
X-RAY DIFFRACTIONf_dihedral_angle_d15.341425
X-RAY DIFFRACTIONf_chiral_restr0.028165
X-RAY DIFFRACTIONf_plane_restr0.001178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1156-2.32810.4111460.35792779X-RAY DIFFRACTION95
2.3281-2.66430.3461540.29062937X-RAY DIFFRACTION99
2.6643-3.35390.31961560.25342967X-RAY DIFFRACTION99
3.3539-19.33530.2241640.17493106X-RAY DIFFRACTION98

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