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- PDB-3psn: Crystal structure of mouse VPS29 complexed with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 3psn
TitleCrystal structure of mouse VPS29 complexed with Mn2+
ComponentsVacuolar protein sorting-associated protein 29Vacuole
KeywordsHYDROLASE / Phosphtase fold / Scaffolding / membrane trafficking / VPS35 / TBC1D5 / SNX1
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 / intracellular membrane-bounded organelle ...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 / intracellular membrane-bounded organelle / 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: 2.4 Å
AuthorsSwarbrick, J. / Shaw, D. / Chhabra, S. / Ghai, R. / Valkov, E. / Norwood, S. / Collins, B.
CitationJournal: To be Published
Title: Conformational dynamics and biomolecular interactions of VPS29 studied by NMR and X-ray crystallography
Authors: Swarbrick, J. / Shaw, D. / Chhabra, S. / Ghai, R. / Valkov, E. / Norwood, S. / Collins, B.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 15, 2010ID: 3LH7
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 29
B: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5838
Polymers43,2542
Non-polymers3306
Water84747
1
A: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7924
Polymers21,6271
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7924
Polymers21,6271
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-23 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.437, 69.122, 69.024
Angle α, β, γ (deg.)90.00, 105.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:182 )
211chain B and (resseq 1:182 )

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Components

#1: Protein Vacuolar protein sorting-associated protein 29 / Vacuole / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QZ88, phosphoserine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 0.1M Tris, 0.2M NaCl, 20% PEG 3350, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.4→19.61 Å / Num. obs: 14590 / % possible obs: 99.7 % / Observed criterion σ(I): 4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z2W

1z2w


Resolution: 2.4→19.171 Å / SU ML: 0.3 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 734 5.03 %random
Rwork0.195 ---
obs0.1973 14590 96.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.551 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.5021 Å2-0 Å26.7353 Å2
2---0.1098 Å20 Å2
3----8.3923 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 6 47 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092969
X-RAY DIFFRACTIONf_angle_d1.1464026
X-RAY DIFFRACTIONf_dihedral_angle_d15.7671084
X-RAY DIFFRACTIONf_chiral_restr0.072459
X-RAY DIFFRACTIONf_plane_restr0.004512
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1446X-RAY DIFFRACTIONPOSITIONAL
12B1446X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.58490.26631430.2144259491
2.5849-2.84430.2971370.2182272095
2.8443-3.25410.25851550.2039279698
3.2541-4.09330.23061480.178284199
4.0933-19.17180.22221510.1913290599

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