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- PDB-1z2x: Crystal structure of mouse Vps29 -

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Basic information

Entry
Database: PDB / ID: 1z2x
TitleCrystal structure of mouse Vps29
ComponentsVacuolar protein sorting 29
KeywordsPROTEIN TRANSPORT / Vps29 / retromer / phosphatase
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / protein transport / endosome membrane / metal ion binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.22 Å
AuthorsCollins, B.M. / Skinner, C.F. / Watson, P.J. / Seaman, M.N.J. / Owen, D.J.
CitationJournal: NAT.STRUCT.MOL.BIOL. / Year: 2005
Title: Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly
Authors: Collins, B.M. / Skinner, C.F. / Watson, P.J. / Seaman, M.N.J. / Owen, D.J.
History
DepositionMar 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting 29
B: Vacuolar protein sorting 29


Theoretical massNumber of molelcules
Total (without water)43,2542
Polymers43,2542
Non-polymers00
Water4,900272
1
A: Vacuolar protein sorting 29


Theoretical massNumber of molelcules
Total (without water)21,6271
Polymers21,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting 29


Theoretical massNumber of molelcules
Total (without water)21,6271
Polymers21,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-23 kcal/mol
Surface area16450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.912, 68.321, 60.166
Angle α, β, γ (deg.)90.00, 106.98, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological unit is beleived to be monomer

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Components

#1: Protein Vacuolar protein sorting 29 / Vesicle protein sorting 29 / Vps29


Mass: 21626.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Plasmid: pGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q9QZ88
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.5 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 0.2M NaCl, 20% PEG3000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 21420 / % possible obs: 99.4 % / Observed criterion σ(I): 6.3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.252 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.22→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.463 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22765 1091 5.1 %RANDOM
Rwork0.17305 ---
obs0.17591 20185 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.347 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å2-1.42 Å2
2---1.64 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 272 3164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212958
X-RAY DIFFRACTIONr_bond_other_d0.0020.022692
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9524010
X-RAY DIFFRACTIONr_angle_other_deg0.93936284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2315362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023252
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02570
X-RAY DIFFRACTIONr_nbd_refined0.2090.2527
X-RAY DIFFRACTIONr_nbd_other0.2480.22985
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.21773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2213
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9641.51808
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77122934
X-RAY DIFFRACTIONr_scbond_it2.50631150
X-RAY DIFFRACTIONr_scangle_it4.0674.51076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.224→2.281 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 71
Rwork0.216 1358

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