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- PDB-2r51: Crystal Structure of mouse Vps26B -

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Basic information

Entry
Database: PDB / ID: 2r51
TitleCrystal Structure of mouse Vps26B
ComponentsVacuolar protein sorting-associated protein 26BVacuole
KeywordsTRANSPORT PROTEIN / retromer / fibronectin III / arrestin domain / Membrane / Phosphorylation / Protein transport / Transport
Function / homology
Function and homology information


retromer complex / retrograde transport, endosome to Golgi / phagocytic vesicle / intracellular protein transport / cellular response to type II interferon / late endosome / early endosome / endosome / 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 / SAD / Resolution: 2.1 Å
AuthorsOwen, D.J. / Teasdale, R.D. / Collins, B.M.
CitationJournal: Traffic / Year: 2008
Title: Structure of Vps26B and mapping of its interaction with the retromer protein complex.
Authors: Collins, B.M. / Norwood, S.J. / Kerr, M.C. / Mahony, D. / Seaman, M.N. / Teasdale, R.D. / Owen, D.J.
History
DepositionSep 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)40,0781
Polymers40,0781
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Vacuolar protein sorting-associated protein 26B

A: Vacuolar protein sorting-associated protein 26B


Theoretical massNumber of molelcules
Total (without water)80,1572
Polymers80,1572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area2060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.755, 125.047, 99.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

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Components

#1: Protein Vacuolar protein sorting-associated protein 26B / Vacuole / Vesicle protein sorting 26B


Mass: 40078.285 Da / Num. of mol.: 1 / Fragment: residues 7-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps26b / Plasmid: pMWKanH6 mVps26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q8C0E2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4 M NaH2PO4, 0.4 M KH2PO4, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9816 Å
DetectorDetector: CCD / Date: Mar 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9816 Å / Relative weight: 1
ReflectionResolution: 2.1→78 Å / Num. obs: 33530 / % possible obs: 99.7 % / Observed criterion σ(I): 2.1 / Redundancy: 10.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.268 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1682 5.1 %RANDOM
Rwork0.19447 ---
obs0.1968 31538 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.297 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--0.35 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 0 249 2640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9643284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3785287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03123.79124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29815467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1581518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021827
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2881
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21572
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.311.51479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83122329
X-RAY DIFFRACTIONr_scbond_it2.70631086
X-RAY DIFFRACTIONr_scangle_it3.9624.5955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 115 -
Rwork0.255 2216 -
obs--96.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0540.07780.04444.68930.35350.3667-0.01430.13420.0792-0.63550.0691-0.2102-0.0892-0.032-0.05480.1086-0.01110.0505-0.2356-0.0168-0.108451.57663.27511.837
20.8553-0.7725-1.00181.62580.72651.2076-0.0837-0.15540.0239-0.10390.0525-0.14570.09210.0320.03120.03020.00560.0531-0.288-0.00410.014660.37126.08211.909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 15813 - 162
2X-RAY DIFFRACTION2AA159 - 296163 - 300

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