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- PDB-1z2w: Crystal structure of mouse Vps29 complexed with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 1z2w
TitleCrystal structure of mouse Vps29 complexed with Mn2+
ComponentsVacuolar protein sorting 29
KeywordsPROTEIN TRANSPORT / Vps29 / retromer / phosphatase / manganese
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 / intracellular protein transport / endosome membrane / endosome / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,93411
Polymers43,2542
Non-polymers6809
Water5,693316
1
A: Vacuolar protein sorting 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0136
Polymers21,6271
Non-polymers3865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9215
Polymers21,6271
Non-polymers2944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-50 kcal/mol
Surface area16910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.914, 68.953, 60.519
Angle α, β, γ (deg.)90.00, 106.65, 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: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.6 Å3/Da / Density % sol: 52.1 %
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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→57 Å / Num. obs: 30024 / % possible obs: 97.6 % / Observed criterion σ(I): 3.7 / Redundancy: 3.5 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.083 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.525 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z2X

1z2x


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.16 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23742 1486 5.1 %RANDOM
Rwork0.17619 ---
obs0.17939 27724 97.44 %-
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: 27.858 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-1.93 Å2
2---0.29 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 34 316 3242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212983
X-RAY DIFFRACTIONr_bond_other_d0.0020.022717
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.9594035
X-RAY DIFFRACTIONr_angle_other_deg1.07336349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6645362
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_restr0.2380.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023252
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02570
X-RAY DIFFRACTIONr_nbd_refined0.2230.2584
X-RAY DIFFRACTIONr_nbd_other0.2610.23049
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0950.21775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2840.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4321.51808
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5822934
X-RAY DIFFRACTIONr_scbond_it3.45931175
X-RAY DIFFRACTIONr_scangle_it5.4274.51101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 110
Rwork0.232 1865

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