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- PDB-6s2s: Hydrogenated human myelin protein P2 at 0.86-A resolution -

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Basic information

Entry
Database: PDB / ID: 6s2s
TitleHydrogenated human myelin protein P2 at 0.86-A resolution
ComponentsMyelin P2 protein
KeywordsLIPID BINDING PROTEIN / FABP / beta barrel / fatty acid
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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / PALMITIC ACID / VACCENIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å
AuthorsLaulumaa, S. / Kursula, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: Molecules / Year: 2019
Title: Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites.
Authors: Laulumaa, S. / Kursula, P.
History
DepositionJun 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Myelin P2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9155
Polymers14,9911
Non-polymers9234
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, the protein is monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint7 kcal/mol
Surface area7310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.930, 57.930, 101.320
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


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.: 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: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 24% PEG6000, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 0.86→50 Å / Num. obs: 137969 / % possible obs: 94.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.068 / Rsym value: 0.063 / Net I/σ(I): 14.7
Reflection shellResolution: 0.86→0.88 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9267 / CC1/2: 0.441 / Rrim(I) all: 1.758 / Rsym value: 1.631 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.10_2140: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bvm

4bvm


Resolution: 0.86→28.965 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 10.07
RfactorNum. reflection% reflection
Rfree0.1178 2770 2.01 %
Rwork0.0991 --
obs0.0994 137907 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.86→28.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 64 306 1418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021436
X-RAY DIFFRACTIONf_angle_d1.8611939
X-RAY DIFFRACTIONf_dihedral_angle_d22.58607
X-RAY DIFFRACTIONf_chiral_restr0.111206
X-RAY DIFFRACTIONf_plane_restr0.013253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.86-0.87490.27671280.28266132X-RAY DIFFRACTION87
0.8749-0.89080.25391320.25396227X-RAY DIFFRACTION88
0.8908-0.90790.24651300.22556262X-RAY DIFFRACTION89
0.9079-0.92640.21641340.19846355X-RAY DIFFRACTION90
0.9264-0.94660.20521250.17316457X-RAY DIFFRACTION91
0.9466-0.96860.18041350.14746508X-RAY DIFFRACTION92
0.9686-0.99280.16841310.12416551X-RAY DIFFRACTION93
0.9928-1.01970.11871330.10816649X-RAY DIFFRACTION94
1.0197-1.04970.10481390.08766679X-RAY DIFFRACTION94
1.0497-1.08360.07431350.06666745X-RAY DIFFRACTION95
1.0836-1.12230.07081400.05526818X-RAY DIFFRACTION95
1.1223-1.16720.06241390.05146855X-RAY DIFFRACTION96
1.1672-1.22040.05851450.05486870X-RAY DIFFRACTION97
1.2204-1.28470.06311390.05716912X-RAY DIFFRACTION96
1.2847-1.36520.07761450.05786974X-RAY DIFFRACTION98
1.3652-1.47060.0851440.06247034X-RAY DIFFRACTION98
1.4706-1.61860.08671460.06787107X-RAY DIFFRACTION98
1.6186-1.85280.10461460.08087129X-RAY DIFFRACTION98
1.8528-2.33410.10811480.09647285X-RAY DIFFRACTION99
2.3341-28.98140.15261560.12877588X-RAY DIFFRACTION99

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