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- PDB-5xce: Crystal structure of Wild type Vps29 from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 5xce
TitleCrystal structure of Wild type Vps29 from Entamoeba histolytica
ComponentsVacuolar protein sorting-associated protein 29Vacuole
KeywordsTRANSPORT PROTEIN / Entamoeba histolytica / Vacuolar protein sorting 29 / Metallophosphatase fold / Calcineurin-like phosphoesterase superfamily domain
Function / homology
Function and homology information


retromer complex / retrograde transport, endosome to Golgi / intracellular protein transport / protein transport / endosome / 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 speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSrivastava, V.K. / Yadav, R. / Tomar, P. / Gourinath, S. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
DST-SERBSB/SO/BB-095/2010 India
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Structural and thermodynamic characterization of metal binding in Vps29 from Entamoeba histolytica: implication in retromer function.
Authors: Srivastava, V.K. / Yadav, R. / Watanabe, N. / Tomar, P. / Mukherjee, M. / Gourinath, S. / Nakada-Tsukui, K. / Nozaki, T. / Datta, S.
History
DepositionMar 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,7542
Polymers43,7542
Non-polymers00
Water5,008278
1
A: Vacuolar protein sorting-associated protein 29


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting-associated protein 29


Theoretical massNumber of molelcules
Total (without water)21,8771
Polymers21,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.564, 78.771, 67.974
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar protein sorting-associated protein 29 / Vacuole


Mass: 21876.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HM-1:IMSS / Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: vsp, EhVPS29, CL6EHI_025270, EHI_025270 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BI08
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM Sodium Acetate, 100mM Sodium cacodylate pH 6.5, 30% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 31246 / % possible obs: 99.9 % / Redundancy: 7.6 % / Net I/σ(I): 39

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Processing

Software
NameVersionClassification
HKL-2000701c3data processing
SCALEPACKdata scaling
PHASERphasing
PHENIX(1.10.1_2155)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w24

1w24


Resolution: 1.86→31.534 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.2471 1571 5.03 %
Rwork0.1979 --
obs0.2004 31246 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→31.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 0 278 3065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012843
X-RAY DIFFRACTIONf_angle_d1.0473864
X-RAY DIFFRACTIONf_dihedral_angle_d15.3761680
X-RAY DIFFRACTIONf_chiral_restr0.066452
X-RAY DIFFRACTIONf_plane_restr0.007497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8605-1.92050.27291290.22172499X-RAY DIFFRACTION92
1.9205-1.98910.28471450.20972678X-RAY DIFFRACTION100
1.9891-2.06880.28471640.20622720X-RAY DIFFRACTION100
2.0688-2.16290.26431410.21052685X-RAY DIFFRACTION100
2.1629-2.27690.28381380.2072705X-RAY DIFFRACTION100
2.2769-2.41950.26061330.20992731X-RAY DIFFRACTION100
2.4195-2.60620.28891430.21332733X-RAY DIFFRACTION100
2.6062-2.86840.29231230.21072742X-RAY DIFFRACTION100
2.8684-3.2830.22291500.20232710X-RAY DIFFRACTION100
3.283-4.13480.22151320.17622751X-RAY DIFFRACTION100
4.1348-31.53850.20711730.18152721X-RAY DIFFRACTION99

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