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- PDB-5xch: Crystal structure of Wild type Vps29 complexed with Zn+2 from Ent... -

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Basic information

Entry
Database: PDB / ID: 5xch
TitleCrystal structure of Wild type Vps29 complexed with Zn+2 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 / cytoplasmic vesicle / 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: 2.85 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0166
Polymers43,7542
Non-polymers2624
Water45025
1
A: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0083
Polymers21,8771
Non-polymers1312
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)22,0083
Polymers21,8771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.310, 47.310, 148.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Vacuolar protein sorting-associated protein 29


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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 % w/v PEG 20000, 20 % v/v PEGMME 550, 0.02 M of alcohol MIX, 0.1 M MES/Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.45
ReflectionResolution: 2.85→40.9 Å / Num. obs: 8561 / % possible obs: 98 % / Redundancy: 11.2 % / Net I/σ(I): 21

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Processing

Software
NameVersionClassification
iMOSFLMdata processing
SCALAdata reduction
PHASERphasing
PHENIX(1.10.1_2155)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCE

5xce


Resolution: 2.85→40.9 Å / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 33.53
RfactorNum. reflection% reflection
Rfree0.3068 411 4.8 %
Rwork0.2867 --
obs0.2879 8561 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.85→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 4 25 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052838
X-RAY DIFFRACTIONf_angle_d0.8423857
X-RAY DIFFRACTIONf_dihedral_angle_d19.7011684
X-RAY DIFFRACTIONf_chiral_restr0.054453
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-30.36411280.30972648X-RAY DIFFRACTION94
3.2744-4.10450.30751490.27932634X-RAY DIFFRACTION94
4.1045-13.16230.29161340.28132653X-RAY DIFFRACTION95

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