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- PDB-5xcj: Crystal structure of Vps29 single mutant (D62A) from Entamoeba hi... -

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Basic information

Entry
Database: PDB / ID: 5xcj
TitleCrystal structure of Vps29 single mutant (D62A) 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 / protein transport / 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: 1.859 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)43,6662
Polymers43,6662
Non-polymers00
Water6,593366
1
A: Vacuolar protein sorting-associated protein 29


Theoretical massNumber of molelcules
Total (without water)21,8331
Polymers21,8331
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)21,8331
Polymers21,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.428, 67.364, 77.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vacuolar protein sorting-associated protein 29


Mass: 21832.959 Da / Num. of mol.: 2 / Mutation: D62A
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.: 366 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
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 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 30853 / % possible obs: 100 % / Redundancy: 4.3 % / Net I/σ(I): 8.5

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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: 1.859→33.729 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.29
RfactorNum. reflection% reflection
Rfree0.2196 1380 4.91 %
Rwork0.2064 --
obs0.2108 28099 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.859→33.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 0 366 3079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072766
X-RAY DIFFRACTIONf_angle_d1.3053765
X-RAY DIFFRACTIONf_dihedral_angle_d19.297961
X-RAY DIFFRACTIONf_chiral_restr0.089446
X-RAY DIFFRACTIONf_plane_restr0.008484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8656-1.93220.2703760.29251797X-RAY DIFFRACTION60
1.9322-2.00960.29231000.25182116X-RAY DIFFRACTION70
2.0096-2.1010.22391350.25842458X-RAY DIFFRACTION80
2.101-2.21180.28171690.25452750X-RAY DIFFRACTION90
2.2118-2.35030.23641300.24212893X-RAY DIFFRACTION95
2.3503-2.53180.2541620.22612904X-RAY DIFFRACTION95
2.5318-2.78640.22271500.23222893X-RAY DIFFRACTION95
2.7864-3.18940.19831430.20832919X-RAY DIFFRACTION95
3.1894-4.01720.18291220.17032959X-RAY DIFFRACTION96
4.0172-33.73480.21011800.18142927X-RAY DIFFRACTION94

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