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- PDB-7bqi: Crystal structure of FYCO1 RUN domain -

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Basic information

Entry
Database: PDB / ID: 7bqi
TitleCrystal structure of FYCO1 RUN domain
ComponentsFYVE and coiled-coil domain-containing protein 1
KeywordsCYTOSOLIC PROTEIN / Autophagy
Function / homology
Function and homology information


plus-end-directed vesicle transport along microtubule / positive regulation of autophagosome maturation / autophagosome / late endosome / lysosome / intracellular membrane-bounded organelle / Golgi apparatus / membrane / metal ion binding
Similarity search - Function
: / : / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger ...: / : / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
FYVE and coiled-coil domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.3 Å
AuthorsSakurai, S. / Shimizu, T. / Ohto, U.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases.
Authors: Sakurai, S. / Shimizu, T. / Ohto, U.
History
DepositionMar 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FYVE and coiled-coil domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)20,8721
Polymers20,8721
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.119, 48.119, 142.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

21A-312-

HOH

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Components

#1: Protein FYVE and coiled-coil domain-containing protein 1 / Zinc finger FYVE domain-containing protein 7


Mass: 20871.553 Da / Num. of mol.: 1 / Fragment: RUN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYCO1, ZFYVE7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQS8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 180mM tri-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 38506 / % possible obs: 90.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 41.6
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1885

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SIRAS
Starting model: SAD model

Resolution: 1.3→45.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 0.948 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1932 5 %RANDOM
Rwork0.2114 ---
obs0.2129 36472 90.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.33 Å2 / Biso mean: 18.731 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.3→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 0 129 1545
Biso mean---27.05 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0191511
X-RAY DIFFRACTIONr_bond_other_d0.0030.021407
X-RAY DIFFRACTIONr_angle_refined_deg2.4341.9552050
X-RAY DIFFRACTIONr_angle_other_deg1.04533250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17524.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74915272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.416159
X-RAY DIFFRACTIONr_chiral_restr0.1590.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
LS refinement shellResolution: 1.3→1.333 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 144 -
Rwork0.276 2662 -
all-2806 -
obs--91.25 %

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