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- PDB-5xck: Crystal structure of Vps29 double mutant (D62A/H86A) from Entamoe... -

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Basic information

Entry
Database: PDB / ID: 5xck
TitleCrystal structure of Vps29 double mutant (D62A/H86A) from Entamoeba histolytica
ComponentsVacuolar protein sorting-associated protein 29
KeywordsPROTEIN TRANSPORT / 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 / 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 speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSrivastava, V.K. / Yadav, R. / Tomar, P. / Gourinath, S. / Datta, S.
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 18, 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)43,5322
Polymers43,5322
Non-polymers00
Water3,963220
1
A: Vacuolar protein sorting-associated protein 29


Theoretical massNumber of molelcules
Total (without water)21,7661
Polymers21,7661
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)21,7661
Polymers21,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.070, 67.441, 77.614
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar protein sorting-associated protein 29


Mass: 21765.889 Da / Num. of mol.: 2 / Mutation: D62A, H86A
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


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
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 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17278 / % possible obs: 93 % / Redundancy: 2.7 % / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
PHENIX(1.10.1_2155)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCE

5xce


Resolution: 2.2→33.636 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34
RfactorNum. reflection% reflection
Rfree0.2788 862 5.11 %
Rwork0.2473 --
obs0.2495 16885 90.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 0 220 3012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032846
X-RAY DIFFRACTIONf_angle_d0.6433867
X-RAY DIFFRACTIONf_dihedral_angle_d18.1831687
X-RAY DIFFRACTIONf_chiral_restr0.046453
X-RAY DIFFRACTIONf_plane_restr0.004498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2005-2.33790.33251250.29572537X-RAY DIFFRACTION83
2.3379-2.51770.30831250.29392653X-RAY DIFFRACTION88
2.5177-2.76970.32931450.28492722X-RAY DIFFRACTION89
2.7697-3.16730.33331520.26382728X-RAY DIFFRACTION89
3.1673-3.97860.26741230.21522714X-RAY DIFFRACTION88
3.9786-15.19580.21461200.22092673X-RAY DIFFRACTION86

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