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- PDB-6cd8: Complex of GID4 fragment with short peptide -

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Basic information

Entry
Database: PDB / ID: 6cd8
TitleComplex of GID4 fragment with short peptide
Components
  • Glucose-induced degradation protein 4 homolog
  • Tetrapeptide PSRV
KeywordsPEPTIDE BINDING PROTEIN / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.3Oct 4, 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: Glucose-induced degradation protein 4 homolog
B: Glucose-induced degradation protein 4 homolog
C: Tetrapeptide PSRV
D: Tetrapeptide PSRV


Theoretical massNumber of molelcules
Total (without water)40,12723
Polymers40,1274
Non-polymers019
Water2,090116
1
A: Glucose-induced degradation protein 4 homolog
C: Tetrapeptide PSRV


Theoretical massNumber of molelcules
Total (without water)20,06313
Polymers20,0632
Non-polymers011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-induced degradation protein 4 homolog
D: Tetrapeptide PSRV


Theoretical massNumber of molelcules
Total (without water)20,06310
Polymers20,0632
Non-polymers08
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.941, 63.941, 289.593
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

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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.: 2 / 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 Tetrapeptide PSRV


Mass: 458.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.13 Å3/Da / Density % sol: 42.24 % / Mosaicity: 0.07 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30% PEG2000 and 0.1M KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.6→48.27 Å / Num. obs: 47911 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Net I/σ(I): 26.9 / Num. measured all: 915253 / 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
1.6-1.6319.81.63847104237923790.8030.3731.681299.7
8.61-48.2714.90.035640443010.0090.0367699.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: early version of PDB entry 6ccr

6ccr


Resolution: 1.6→48.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.129 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.093
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2237 2382 5 %
Rwork0.1969 --
obs0.1982 45300 99.99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.7 Å2 / Biso mean: 30.639 Å2 / Biso min: 15.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å2-0 Å2
2---0.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.6→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 19 116 2876
Biso mean--31.27 33.34 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192906
X-RAY DIFFRACTIONr_bond_other_d0.0020.022408
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9093955
X-RAY DIFFRACTIONr_angle_other_deg0.94635579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11923.642151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66215431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.958159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_mcbond_it0.8261.5461381
X-RAY DIFFRACTIONr_mcbond_other0.8241.5451380
X-RAY DIFFRACTIONr_mcangle_it1.3032.3171727
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 177 -
Rwork0.269 3245 -
all-3422 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2766-0.2582-0.63892.59360.12263.09170.02240.11490.0628-0.0543-0.09790.0024-0.3075-0.20270.07540.14650.0424-0.01350.024-0.00290.00525.299970.71780.382
23.4962-0.5660.99372.0619-0.032.2361-0.03170.2004-0.0179-0.16270.0095-0.0808-0.00720.28470.02210.1131-0.04390.00730.21730.01070.00659.181357.835223.407
37.8699-3.43831.21717.69161.21482.54460.0215-0.0723-0.23410.2041-0.0117-0.04560.21360.2038-0.00980.15120.0248-0.00720.14210.01690.148137.984763.4224.5792
43.9922-3.26492.4425.9068-4.06347.77960.03670.2386-0.0365-0.1586-0.17280.21-0.07890.07710.1360.1645-0.0047-0.01410.17110.0020.131748.296363.102715.3888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 289
2X-RAY DIFFRACTION2B125 - 289
3X-RAY DIFFRACTION3C1 - 4
4X-RAY DIFFRACTION4D1 - 4

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