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- PDB-1vfy: PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PR... -

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Basic information

Entry
Database: PDB / ID: 1vfy
TitlePHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PROTEIN FROM SACCHAROMYCES CEREVISIAE
ComponentsPHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF PROTEIN VPS27
KeywordsTRANSPORT PROTEIN / FYVE DOMAIN / ENDOSOME MATURATION / INTRACELLULAR TRAFFICKING
Function / homology
Function and homology information


microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport ...microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / vacuolar membrane / protein secretion / ubiquitin binding / endosome membrane / endosome / protein heterodimerization activity / protein domain specific binding / protein-containing complex / metal ion binding
Similarity search - Function
: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 27
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å
AuthorsHurley, J.H. / Misra, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p.
Authors: Misra, S. / Hurley, J.H.
History
DepositionApr 26, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF PROTEIN VPS27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4023
Polymers8,2711
Non-polymers1312
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.090, 26.570, 31.610
Angle α, β, γ (deg.)111.79, 92.70, 105.70
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF PROTEIN VPS27


Mass: 8271.317 Da / Num. of mol.: 1 / Fragment: 163-229, FYVE DOMAIN / Mutation: 6 RESIDUES (EFIVTD) INSERTED AT C-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: CYTOPLASM, ENDOSOMAL MEMBRANES / Gene: VPS27 / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P40343
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.16 Å3/Da / Density % sol: 38 %
Crystal growpH: 5.6
Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.6, 15% PEG 4000, pH 5.6
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-15 mg/mlprotein1drop
220 mMTris-HCl1drop
310 mMdithiothreitol1drop
40.2 Mammonium acetate1reservoir
50.1 Msodium acetate1reservoir
615 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.2830,1.2822,1.2320
DetectorType: ADSC / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2831
21.28221
31.2321
ReflectionResolution: 1.15→30 Å / Num. all: 21646 / Num. obs: 20972 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 8 / Rsym value: 0.011 / % possible all: 82.3
Reflection
*PLUS

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.15→30 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.181 977 4 %RANDOM
Rwork0.174 ---
all-20972 --
obs-20972 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.119 Å20.176 Å20.537 Å2
2--0.786 Å21.795 Å2
3----0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.12 Å
Luzzati d res low-6 Å
Luzzati sigma a0.07 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms532 0 2 109 643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.57
X-RAY DIFFRACTIONc_mcangle_it2.2
X-RAY DIFFRACTIONc_scbond_it3.43
X-RAY DIFFRACTIONc_scangle_it4.86
LS refinement shellResolution: 1.15→1.19 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.248 67 2.8 %
Rwork0.213 1609 -
obs--69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMGENERATE_9.MTF
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PARAM19.ION

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