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- PDB-4l9c: Crystal structure of the FP domain of human F-box protein Fbxo7 (... -

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Basic information

Entry
Database: PDB / ID: 4l9c
TitleCrystal structure of the FP domain of human F-box protein Fbxo7 (native)
ComponentsF-box only protein 7
KeywordsPROTEIN BINDING / alpha/beta fold
Function / homology
Function and homology information


negative regulation of lymphocyte differentiation / glial cytoplasmic inclusion / classical Lewy body / Lewy neurite / Lewy body corona / Lewy body core / positive regulation of autophagy of mitochondrion / lymphocyte differentiation / autophagy of mitochondrion / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway ...negative regulation of lymphocyte differentiation / glial cytoplasmic inclusion / classical Lewy body / Lewy neurite / Lewy body corona / Lewy body core / positive regulation of autophagy of mitochondrion / lymphocyte differentiation / autophagy of mitochondrion / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / protein targeting to mitochondrion / regulation of locomotion / SCF ubiquitin ligase complex / negative regulation of G1/S transition of mitotic cell cycle / regulation of neuron projection development / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / ubiquitin ligase complex / ubiquitin binding / regulation of protein stability / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein heterodimerization activity / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Protein Transport Mog1p; Chain A - #30 / PI31 proteasome regulator, N-terminal / PI31 proteasome regulator N-terminal / Protein Transport Mog1p; Chain A / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain ...: / Protein Transport Mog1p; Chain A - #30 / PI31 proteasome regulator, N-terminal / PI31 proteasome regulator N-terminal / Protein Transport Mog1p; Chain A / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
F-box only protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDu, Z. / Huang, X. / Shang, J. / Yang, Y. / Wang, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the FP domain of Fbxo7 reveals a novel mode of protein-protein interaction.
Authors: Shang, J. / Wang, G. / Yang, Y. / Huang, X. / Du, Z.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box only protein 7
B: F-box only protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6163
Polymers35,5232
Non-polymers921
Water1,72996
1
A: F-box only protein 7


Theoretical massNumber of molelcules
Total (without water)17,7621
Polymers17,7621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F-box only protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8542
Polymers17,7621
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: F-box only protein 7
hetero molecules

A: F-box only protein 7


Theoretical massNumber of molelcules
Total (without water)35,6163
Polymers35,5232
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area2110 Å2
ΔGint-11 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.220, 64.410, 89.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein F-box only protein 7


Mass: 17761.744 Da / Num. of mol.: 2 / Fragment: unp residues 180-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBX7, FBXO7, HUMAN FBXO7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y3I1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.79 Å3/Da / Density % sol: 31.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, MES 7.2, KBr , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 15476

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.628 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8234 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1544 10 %
Rwork0.1909 --
obs0.1965 15439 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.45 Å2 / Biso mean: 32.2989 Å2 / Biso min: 6.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 6 96 2464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042409
X-RAY DIFFRACTIONf_angle_d0.8573263
X-RAY DIFFRACTIONf_chiral_restr0.057388
X-RAY DIFFRACTIONf_plane_restr0.003408
X-RAY DIFFRACTIONf_dihedral_angle_d13.917908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.16780.34171380.22961238137699
2.1678-2.24530.27931350.221112261361100
2.2453-2.33520.30921390.212212441383100
2.3352-2.44150.25381380.213312421380100
2.4415-2.57020.27321400.194912571397100
2.5702-2.73120.27251380.203712341372100
2.7312-2.9420.25181400.204212671407100
2.942-3.23790.28611390.203812571396100
3.2379-3.70610.21191430.180212811424100
3.7061-4.66820.22591430.168812831426100
4.6682-39.63550.21151510.17691366151799

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