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- PDB-5ltg: Citrate-bound Pichia angusta Atg18 -

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Basic information

Entry
Database: PDB / ID: 5ltg
TitleCitrate-bound Pichia angusta Atg18
ComponentsAutophagy-related protein 18
KeywordsLIPID BINDING PROTEIN / membrane binding 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
CITRATE ANION / PHOSPHATE ION / Autophagy-related protein 18
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsScacioc, A. / Kuhnel, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: To Be Published
Title: Citrate-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

Downloads & links

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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)116,5786
Polymers116,0102
Non-polymers5684
Water6,936385
1
A: Autophagy-related protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2893
Polymers58,0051
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Autophagy-related protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2893
Polymers58,0051
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.811, 57.969, 62.173
Angle α, β, γ (deg.)84.19, 81.23, 87.01
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
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.: 2 / Source method: isolated from a natural source / Formula: PO4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 1.76 Å3/Da / Density % sol: 30.3 %
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.342 Å / Num. obs: 51797 / % possible obs: 94.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.361

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AV8

4av8


Resolution: 2→41.342 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 2570 5 %
Rwork0.214 --
obs0.2167 51378 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 36 385 5238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014965
X-RAY DIFFRACTIONf_angle_d1.2046754
X-RAY DIFFRACTIONf_dihedral_angle_d11.8641792
X-RAY DIFFRACTIONf_chiral_restr0.054800
X-RAY DIFFRACTIONf_plane_restr0.005856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03850.36931370.28942592X-RAY DIFFRACTION94
2.0385-2.08010.33741420.26992724X-RAY DIFFRACTION95
2.0801-2.12530.36041420.25712696X-RAY DIFFRACTION96
2.1253-2.17480.3231430.24852708X-RAY DIFFRACTION96
2.1748-2.22920.3131430.23932721X-RAY DIFFRACTION95
2.2292-2.28940.26641400.22512665X-RAY DIFFRACTION95
2.2894-2.35680.31961420.2382694X-RAY DIFFRACTION96
2.3568-2.43280.2771440.22242734X-RAY DIFFRACTION97
2.4328-2.51980.26431440.22072738X-RAY DIFFRACTION96
2.5198-2.62070.28261440.23422722X-RAY DIFFRACTION96
2.6207-2.73990.32071440.24132746X-RAY DIFFRACTION96
2.7399-2.88430.30281430.22172705X-RAY DIFFRACTION96
2.8843-3.0650.27851430.22262731X-RAY DIFFRACTION97
3.065-3.30150.27341440.21822720X-RAY DIFFRACTION97
3.3015-3.63360.24011440.19832746X-RAY DIFFRACTION97
3.6336-4.1590.23131460.18392764X-RAY DIFFRACTION97
4.159-5.23820.21351430.16972716X-RAY DIFFRACTION96
5.2382-41.35040.2581420.22182686X-RAY DIFFRACTION95

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