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- PDB-4d6a: Human myelin protein P2 after neutron scattering experiments -

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Basic information

Entry
Database: PDB / ID: 4d6a
TitleHuman myelin protein P2 after neutron scattering experiments
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 domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLaulumaa, S. / Natali, F. / 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 1.2Jan 17, 2018Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)15,6644
Polymers15,0231
Non-polymers6413
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.670, 57.670, 100.660
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: 15023.470 Da / Num. of mol.: 1
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.84 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9444
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9444 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 30872 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 18.44 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.9
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.3 / % possible all: 99.9

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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: 1.45→29.002 Å / SU ML: 0.14 / σ(F): 2 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 1540 5 %
Rwork0.1469 --
obs0.1488 30806 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→29.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 44 180 1286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091164
X-RAY DIFFRACTIONf_angle_d1.3241565
X-RAY DIFFRACTIONf_dihedral_angle_d19.981468
X-RAY DIFFRACTIONf_chiral_restr0.07177
X-RAY DIFFRACTIONf_plane_restr0.005196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.49680.32321360.26542590X-RAY DIFFRACTION100
1.4968-1.55030.30091380.21152618X-RAY DIFFRACTION100
1.5503-1.61230.2091380.17332620X-RAY DIFFRACTION100
1.6123-1.68570.21181380.15372620X-RAY DIFFRACTION100
1.6857-1.77460.18221390.13262630X-RAY DIFFRACTION100
1.7746-1.88570.15431370.12142629X-RAY DIFFRACTION100
1.8857-2.03130.17181400.11722649X-RAY DIFFRACTION100
2.0313-2.23570.17241410.12492669X-RAY DIFFRACTION100
2.2357-2.5590.18691410.1382680X-RAY DIFFRACTION100
2.559-3.22340.17941430.15292726X-RAY DIFFRACTION100
3.2234-29.00760.1731490.152835X-RAY DIFFRACTION98

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