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- PDB-5b4n: Structure analysis of function associated loop mutant of substrat... -

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Basic information

Entry
Database: PDB / ID: 5b4n
TitleStructure analysis of function associated loop mutant of substrate recognition domain of Fbs1 ubiquitin ligase
ComponentsF-box only protein 2
KeywordsLIGASE / SCF E3 ubiquitin ligase / F-box protein / glycoproteins / sequence-structure relationship
Function / homology
Function and homology information


extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of protein ubiquitination / ERAD pathway ...extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of protein ubiquitination / ERAD pathway / amyloid-beta binding / ubiquitin-dependent protein catabolic process / carbohydrate binding / dendritic spine / protein ubiquitination / negative regulation of cell population proliferation / glutamatergic synapse / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Galactose-binding domain-like ...F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
F-box only protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNishio, K. / Yoshida, Y. / Tanaka, K. / Mizushima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology of Japan24112009 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structural analysis of a function-associated loop mutant of the substrate-recognition domain of Fbs1 ubiquitin ligase
Authors: Nishio, K. / Yoshida, Y. / Tanaka, K. / Mizushima, T.
History
DepositionApr 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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: F-box only protein 2
B: F-box only protein 2


Theoretical massNumber of molelcules
Total (without water)47,2522
Polymers47,2522
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint2 kcal/mol
Surface area17030 Å2
Unit cell
Length a, b, c (Å)44.541, 96.203, 44.681
Angle α, β, γ (deg.)90.00, 101.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein F-box only protein 2


Mass: 23626.201 Da / Num. of mol.: 2 / Fragment: UNP residues 117-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fbxo2, Fbs1, Fbx2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q80UW2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 37.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20%PEG 3,350, 1%Tryptone and 0.05M HEPES-Na (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 16552 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 22.6
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.436

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1umh

1umh


Resolution: 2.3→39.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.003 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26571 832 5.1 %RANDOM
Rwork0.18482 ---
obs0.18882 15586 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.256 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å20.01 Å2
2--0.06 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 0 93 2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9294010
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69524.074162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1315468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0111522
X-RAY DIFFRACTIONr_chiral_restr0.120.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212350
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6142.9171390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2544.361734
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.323.2851556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.72225.3454480
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 73 -
Rwork0.254 1151 -
obs--100 %

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