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- PDB-1xb4: Crystal structure of subunit VPS25 of the endosomal trafficking c... -

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Basic information

Entry
Database: PDB / ID: 1xb4
TitleCrystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II
ComponentsHypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
KeywordsUNKNOWN FUNCTION / winged helix
Function / homology
Function and homology information


ESCRT II complex / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / ATP export / Endosomal Sorting Complex Required For Transport (ESCRT) / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / structural molecule activity / protein homodimerization activity / cytosol
Similarity search - Function
"Winged helix" DNA-binding domain. Chain C. Domain 1 / ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein-sorting-associated protein 25
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsWeissenhorn, W. / Wernimont, A.K.
CitationJournal: BMC Struct.Biol. / Year: 2004
Title: Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II.
Authors: Wernimont, A.K. / Weissenhorn, W.
History
DepositionAug 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
B: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
C: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
D: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region


Theoretical massNumber of molelcules
Total (without water)94,3314
Polymers94,3314
Non-polymers00
Water28816
1
A: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
B: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region


Theoretical massNumber of molelcules
Total (without water)47,1652
Polymers47,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-12 kcal/mol
Surface area18540 Å2
MethodPISA
2
C: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region
D: Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region


Theoretical massNumber of molelcules
Total (without water)47,1652
Polymers47,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-12 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.360, 123.660, 140.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hypothetical 23.6 kDa protein in YUH1-URA8 intergenic region / Vps25


Mass: 23582.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YJR102C, J1957 / Production host: Escherichia coli (E. coli) / References: UniProt: P47142
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, Magnesium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.97914
SYNCHROTRONESRF ID14-320.931
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979141
20.9311
ReflectionResolution: 3.05→27.4 Å / Num. obs: 18350

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Processing

Software
NameVersionClassification
ProDCdata collection
XDSdata reduction
SOLVEphasing
CNS1refinement
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.327 790 -random
Rwork0.327 ---
all0.273 17504 --
obs0.273 16404 93.7 %-
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5757 0 0 16 5773

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