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- PDB-6cdg: GID4 fragment in complex with a peptide -

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Basic information

Entry
Database: PDB / ID: 6cdg
TitleGID4 fragment in complex with a peptide
Components
  • Glucose-induced degradation protein 4 homolog
  • Hexapeptide PGLWKS
KeywordsPEPTIDE BINDING PROTEIN / structural genomics consortium / SGC
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsDong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway.
Authors: Dong, C. / Zhang, H. / Li, L. / Tempel, W. / Loppnau, P. / Min, J.
History
DepositionFeb 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 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 1.4Apr 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: Glucose-induced degradation protein 4 homolog
B: Hexapeptide PGLWKS


Theoretical massNumber of molelcules
Total (without water)20,29313
Polymers20,2932
Non-polymers011
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.993, 40.651, 56.717
Angle α, β, γ (deg.)90.000, 98.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19604.777 Da / Num. of mol.: 1 / Fragment: residues 124-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVV7
#2: Protein/peptide Hexapeptide PGLWKS


Mass: 687.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.08 Å3/Da / Density % sol: 40.84 % / Mosaicity: 0.19 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40.65 Å / Num. obs: 21138 / % possible obs: 95.4 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.046 / Rrim(I) all: 0.089 / Net I/σ(I): 13.1 / Num. measured all: 77760 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.633.61.3513667100810080.4240.8141.5811.190.5
8.77-40.653.10.0194641510.9990.0130.02359.797.7

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: an unpublished, nearly isomorphous crystal structure of GID4

Resolution: 1.6→32.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.275 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.111
Details: The starting model from a nearly isomorphous starting model could be refined without molecular replacement search.
RfactorNum. reflection% reflection
Rfree0.2483 1078 5.1 %
Rwork0.2095 --
obs0.2114 20015 95.3 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.69 Å2 / Biso mean: 21.326 Å2 / Biso min: 9.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.87 Å2
2---0.77 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: final / Resolution: 1.6→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 11 59 1426
Biso mean--21.83 25.7 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191435
X-RAY DIFFRACTIONr_bond_other_d0.0020.021210
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.911950
X-RAY DIFFRACTIONr_angle_other_deg0.96232792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3755175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59523.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27215213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.108154
X-RAY DIFFRACTIONr_chiral_restr0.1010.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02347
X-RAY DIFFRACTIONr_mcbond_it1.6892.196686
X-RAY DIFFRACTIONr_mcbond_other1.6792.192685
X-RAY DIFFRACTIONr_mcangle_it2.6443.269856
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 70 -
Rwork0.353 1367 -
all-1437 -
obs--90.32 %

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