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- PDB-5ltd: Phosphate-bound Pichia angusta Atg18 -

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Basic information

Entry
Database: PDB / ID: 5ltd
TitlePhosphate-bound Pichia angusta Atg18
ComponentsAutophagy-related protein 18
KeywordsLIPID BINDING PROTEIN / membrane bound protein
Function / homology
Function and homology information


phagophore assembly site membrane / vacuolar membrane / autophagy / protein transport / endosome membrane
Similarity search - Function
: / PROPPIN / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Autophagy-related protein 18
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsScacioc, A. / Kuhnel, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: To Be Published
Title: Phopshate-bound Pichia angusta Atg18
Authors: Scacioc, A. / Kuhnel, K.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Autophagy-related protein 18
B: Autophagy-related protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4527
Polymers116,0102
Non-polymers4425
Water2,144119
1
A: Autophagy-related protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1953
Polymers58,0051
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Autophagy-related protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2574
Polymers58,0051
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.242, 58.253, 62.250
Angle α, β, γ (deg.)83.73, 80.85, 86.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Autophagy-related protein 18


Mass: 58005.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: two phosphate ions bound as ligands to the protein / Source: (gene. exp.) Pichia angusta (fungus) / Gene: ATG18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5QA94
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20 % (w/V) PEG 8000, 0.2 M NaCl, 0.1 M sodium phosphate dibasic-citric acid pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 27376 / % possible obs: 98.3 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.8
Reflection shellRmerge(I) obs: 0.645 / % possible all: 96.5

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTG

5ltg


Resolution: 2.5→45 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.265 --
Rwork0.221 --
obs-27376 98.3 %
Refinement stepCycle: LAST / Resolution: 2.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 24 119 4881

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