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- PDB-2rkk: Crystal Structure of S.cerevisiae Vta1 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2rkk
TitleCrystal Structure of S.cerevisiae Vta1 N-terminal domain
ComponentsVacuolar protein sorting-associated protein VTA1Vacuole
KeywordsLIPID TRANSPORT / MIT motif / Cytoplasm / Endosome / Membrane / Protein transport / Transport
Function / homology
Function and homology information


ESCRT IV complex / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / late endosome to vacuole transport / lipid transport / ATPase activator activity / multivesicular body / protein transport / protein-macromolecule adaptor activity / endosome
Similarity search - Function
Vacuolar protein sorting-associated protein vta1 / Vta1/Callose synthase, N-terminal domain superfamily / Vta1/callose synthase, N-terminal / Vta1, C-terminal / Vacuolar protein sorting-associated protein Vta1-like / Vta1 like / Vta1 C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein VTA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.9 Å
AuthorsXiao, J. / Xia, H. / Zhou, J. / Xu, Z.
CitationJournal: Dev.Cell / Year: 2008
Title: Structural basis of vta1 function in the multivesicular body sorting pathway.
Authors: Xiao, J. / Xia, H. / Zhou, J. / Azmi, I.F. / Davies, B.A. / Katzmann, D.J. / Xu, Z.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein VTA1
B: Vacuolar protein sorting-associated protein VTA1


Theoretical massNumber of molelcules
Total (without water)38,2982
Polymers38,2982
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.169, 126.169, 70.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Vacuolar protein sorting-associated protein VTA1 / Vacuole / VPS20-associated protein 1


Mass: 19149.123 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VTA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06263
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.65 Å3/Da / Density % sol: 66.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: Sodium Formate, vapor diffusion, temperature 293K, pH 7, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 9.7 % / Av σ(I) over netI: 11 / Number: 101963 / Rmerge(I) obs: 0.081 / Χ2: 2.13 / D res high: 3 Å / D res low: 50 Å / Num. obs: 10527 / % possible obs: 95.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465099.610.0557.6759.8
5.136.4610010.0793.10910.1
4.485.1310010.0622.11210.2
4.074.4810010.0791.66410.2
3.784.0710010.1031.310.2
3.563.7810010.1450.95910.1
3.383.5697.810.2050.859.8
3.233.3894.910.3320.829.4
3.113.2385.710.4140.768.8
33.117310.4870.7397.4
ReflectionResolution: 2.9→50 Å / Num. obs: 12169 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.062 / Χ2: 1.325 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-370.41811640.61696.7
3-3.127.50.30111960.67499.3
3.12-3.277.70.21712280.801100
3.27-3.447.60.14912080.908100
3.44-3.657.60.10712111.212100
3.65-3.947.50.08212201.546100
3.94-4.337.30.06712301.992100
4.33-4.967.20.05612172.13299.9
4.96-6.247.50.04912361.61100
6.24-507.10.03312591.74699.3

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
CNSrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→50 Å / FOM work R set: 0.79 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 602 4.9 %
Rwork0.215 --
obs-11746 94.8 %
Solvent computationBsol: 64.107 Å2
Displacement parametersBiso mean: 81.482 Å2
Baniso -1Baniso -2Baniso -3
1--11.795 Å20 Å20 Å2
2---11.795 Å20 Å2
3---23.591 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 11 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.108
X-RAY DIFFRACTIONc_mcbond_it1.4941.5
X-RAY DIFFRACTIONc_scbond_it1.8572
X-RAY DIFFRACTIONc_mcangle_it2.6912
X-RAY DIFFRACTIONc_scangle_it3.0822.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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