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- PDB-7q4y: human Gid4 bound to a Gly/N-peptide -

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Basic information

Entry
Database: PDB / ID: 7q4y
Titlehuman Gid4 bound to a Gly/N-peptide
ComponentsGlucose-induced degradation protein 4 homolog
KeywordsLIGASE / GID / CTLH / ubiquitin / E3 ligase
Function / homologyVacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / Regulation of pyruvate metabolism / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cytosol / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsSherpa, D. / Chrustowicz, J. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
German Research Foundation (DFG)SCHU 3196/1 Germany
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Multifaceted N-Degron Recognition and Ubiquitylation by GID/CTLH E3 Ligases.
Authors: Chrustowicz, J. / Sherpa, D. / Teyra, J. / Loke, M.S. / Popowicz, G.M. / Basquin, J. / Sattler, M. / Prabu, J.R. / Sidhu, S.S. / Schulman, B.A.
History
DepositionNov 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-induced degradation protein 4 homolog
B: Glucose-induced degradation protein 4 homolog


Theoretical massNumber of molelcules
Total (without water)47,1662
Polymers47,1662
Non-polymers00
Water48627
1
A: Glucose-induced degradation protein 4 homolog


Theoretical massNumber of molelcules
Total (without water)23,5831
Polymers23,5831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-induced degradation protein 4 homolog


Theoretical massNumber of molelcules
Total (without water)23,5831
Polymers23,5831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.023, 72.023, 146.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Glucose-induced degradation protein 4 homolog / Vacuolar import and degradation protein 24 homolog


Mass: 23583.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IVV7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG 3350, 0.2 M ammonium nitrate, 0.1 M Bis-Tris pH 7

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 3.08→73.16 Å / Num. obs: 15664 / % possible obs: 99.1 % / Redundancy: 5.7 % / CC1/2: 0.994 / Net I/σ(I): 8.8
Reflection shellResolution: 3.08→3.26 Å / Num. unique obs: 2435 / CC1/2: 0.236

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CDC

6cdc


Resolution: 3.08→62.37 Å / Cross valid method: THROUGHOUT / σ(F): 85.11 / Phase error: 27.48 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2645 782 5.01 %
Rwork0.2445 --
obs0.251 15596 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→62.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 0 27 2737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022798
X-RAY DIFFRACTIONf_angle_d0.4863802
X-RAY DIFFRACTIONf_dihedral_angle_d4.405373
X-RAY DIFFRACTIONf_chiral_restr0.041383
X-RAY DIFFRACTIONf_plane_restr0.003489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.270.28771290.29452411X-RAY DIFFRACTION90
3.27-3.520.30261280.28532442X-RAY DIFFRACTION95
3.52-3.880.31781310.29052511X-RAY DIFFRACTION95
3.88-4.440.25561310.23662485X-RAY DIFFRACTION95
4.44-5.590.2541320.2152481X-RAY DIFFRACTION95
5.6-62.370.27771310.24892484X-RAY DIFFRACTION95

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