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- PDB-6ccr: Selenomethionyl derivative of a GID4 fragment -

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Basic information

Entry
Database: PDB / ID: 6ccr
TitleSelenomethionyl derivative of a GID4 fragment
ComponentsGlucose-induced degradation protein 4 homolog
KeywordsPROTEIN BINDING / Structural Genomics / 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)
MethodX-RAY DIFFRACTION / SAD / 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 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Glucose-induced degradation protein 4 homolog


Theoretical massNumber of molelcules
Total (without water)21,78637
Polymers21,7861
Non-polymers036
Water2,720151
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.167, 39.986, 129.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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


Mass: 21786.072 Da / Num. of mol.: 1 / Fragment: residues 116-300
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: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 36 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.7 % / Mosaicity: 0.16 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% 2-propanol, 20% PEG4K and 0.1M Na-HEPES

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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: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→43 Å / Num. all: 315373 / Num. obs: 23452 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.05 / Net I/σ(I): 41.7 / Num. measured all: 315373 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6312.80.2561426914269111111110.9830.0730.26711.198.7
8.77-4310.20.02419311890.9990.0080.02581.399.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
SHELXDphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.344 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the structure was phased by SAD with the SHELX/PHASER/PARROT pipeline and automatically traced with ARP/wARP.
RfactorNum. reflection% reflection
Rfree0.1869 1155 4.9 %
Rwork0.1587 --
obs0.1601 22235 99.95 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 38.3 Å2 / Biso mean: 9.917 Å2 / Biso min: 1.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-0 Å2
2---0.46 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 1.6→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 36 151 1704
Biso mean--16.49 18.88 -
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191603
X-RAY DIFFRACTIONr_bond_other_d0.0020.021346
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9212184
X-RAY DIFFRACTIONr_angle_other_deg0.94833134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05123.73583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.98615243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.352155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021843
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02382
X-RAY DIFFRACTIONr_mcbond_it0.8490.915760
X-RAY DIFFRACTIONr_mcbond_other0.8490.915759
X-RAY DIFFRACTIONr_mcangle_it1.3181.377953
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 81 -
Rwork0.158 1579 -
all-1660 -
obs--99.52 %

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