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- PDB-4exv: Structure of Kluyveromyces lactis Hsv2p -

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Basic information

Entry
Database: PDB / ID: 4exv
TitleStructure of Kluyveromyces lactis Hsv2p
ComponentsSVP1-like protein 2
KeywordsTRANSPORT PROTEIN / PROPPIN / WD-repeat / Phosphoinosides / Phosphatidylinositol / phosphate binding / Autophagy / Atg2 / Atg9 / Atg21
Function / homology
Function and homology information


nucleophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / vacuolar membrane / extrinsic component of membrane / autophagy of mitochondrion / cytoplasmic vesicle membrane / protein transport / cytosol
Similarity search - Function
: / PROPPIN / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsBaskaran, S. / Hurley, J.H.
CitationJournal: Mol.Cell / Year: 2012
Title: Two-Site Recognition of Phosphatidylinositol 3-Phosphate by PROPPINs in Autophagy.
Authors: Baskaran, S. / Ragusa, M.J. / Boura, E. / Hurley, J.H.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SVP1-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5084
Polymers39,2201
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.236, 157.236, 157.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein SVP1-like protein 2


Mass: 39219.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: HSV2, KLLA0E15972g / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q6CN23
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 4.13 Å3/Da / Density % sol: 70.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 50 mM MES pH 6.2, 1.8 M Magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13828 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 85.19 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 3→49.72 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / σ(F): 1.33 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 688 5 %
Rwork0.218 --
obs0.221 13757 99.7 %
all-13828 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.17 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 79.15 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 3→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 15 0 2554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092600
X-RAY DIFFRACTIONf_angle_d1.2733523
X-RAY DIFFRACTIONf_dihedral_angle_d18.68943
X-RAY DIFFRACTIONf_chiral_restr0.086393
X-RAY DIFFRACTIONf_plane_restr0.005446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23570.36751360.29942529X-RAY DIFFRACTION100
3.2357-3.56130.34011560.24442527X-RAY DIFFRACTION100
3.5613-4.07640.25991410.2162577X-RAY DIFFRACTION99
4.0764-5.1350.2491230.17642630X-RAY DIFFRACTION100
5.135-49.72920.24351320.22942806X-RAY DIFFRACTION100

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