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- PDB-3lh9: Crystal structure of mouse VPS26B(L197S/R199E) in spacegroup P41 21 2 -

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Basic information

Entry
Database: PDB / ID: 3lh9
TitleCrystal structure of mouse VPS26B(L197S/R199E) in spacegroup P41 21 2
ComponentsVacuolar protein sorting-associated protein 26B
KeywordsPROTEIN TRANSPORT / arrestin / fibronectin / Membrane / Transport
Function / homology
Function and homology information


postsynaptic early endosome / postsynaptic recycling endosome / retromer complex / retrograde transport, endosome to Golgi / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / phagocytic vesicle / intracellular protein transport / cellular response to type II interferon / late endosome / early endosome ...postsynaptic early endosome / postsynaptic recycling endosome / retromer complex / retrograde transport, endosome to Golgi / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / phagocytic vesicle / intracellular protein transport / cellular response to type II interferon / late endosome / early endosome / glutamatergic synapse / cytosol
Similarity search - Function
Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Immunoglobulin-like - #640 / Arrestin-like, C-terminal / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 26B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCollins, B. / Shaw, D. / Norwood, S.
CitationJournal: Traffic / Year: 2011
Title: Assembly and solution structure of the core retromer protein complex.
Authors: Norwood, S.J. / Shaw, D.J. / Cowieson, N.P. / Owen, D.J. / Teasdale, R.D. / Collins, B.M.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: 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: Vacuolar protein sorting-associated protein 26B
B: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)79,2982
Polymers79,2982
Non-polymers00
Water5,549308
1
A: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)39,6491
Polymers39,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)39,6491
Polymers39,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.350, 118.350, 214.513
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 Vacuolar protein sorting-associated protein 26B / Vesicle protein sorting 26B


Mass: 39648.973 Da / Num. of mol.: 2 / Fragment: UNP residues 7-336 / Mutation: L197S,R199E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8C0E2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 4.74 Å3/Da / Density % sol: 74.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorDetector: CCD / Date: Nov 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.4→45.2 Å / Num. obs: 60249 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 62.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 3 / Num. unique all: 5584 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R51

2r51


Resolution: 2.4→42.541 Å / SU ML: 0.34 / σ(F): 1.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 3041 5.05 %
Rwork0.1986 --
obs0.2001 60249 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.914 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→42.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 0 308 5065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084868
X-RAY DIFFRACTIONf_angle_d1.1696554
X-RAY DIFFRACTIONf_dihedral_angle_d19.0431836
X-RAY DIFFRACTIONf_chiral_restr0.08711
X-RAY DIFFRACTIONf_plane_restr0.004838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.32053180.27245584X-RAY DIFFRACTION100
2.4858-2.58530.27693010.24555643X-RAY DIFFRACTION100
2.5853-2.70290.26992890.24045634X-RAY DIFFRACTION100
2.7029-2.84540.30483060.235651X-RAY DIFFRACTION100
2.8454-3.02360.27212800.2325693X-RAY DIFFRACTION100
3.0236-3.2570.24952980.22115674X-RAY DIFFRACTION100
3.257-3.58460.23233070.19925714X-RAY DIFFRACTION100
3.5846-4.1030.20622820.17515765X-RAY DIFFRACTION100
4.103-5.16790.16133230.14115799X-RAY DIFFRACTION100
5.1679-42.54810.22393370.20746051X-RAY DIFFRACTION100

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