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- PDB-7slz: CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596 -

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Basic information

Entry
Database: PDB / ID: 7slz
TitleCRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596
ComponentsGlucose-induced degradation protein 4 homolog
KeywordsPEPTIDE BINDING PROTEIN / Pro/N-degron / protein degradation / 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 / Chem-9QU / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsSong, X. / Dong, A. / Calabrese, M. / Wang, F. / Owen, D. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH BPF023596
Authors: Song, X. / Dong, A. / Calabrese, M. / Wang, F. / Owen, D. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionOct 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0062
Polymers19,6051
Non-polymers4021
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.264, 40.264, 202.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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
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 BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: Q8IVV7
#2: Chemical ChemComp-9QU / N-[(1s,4s)-4-(1H-benzimidazol-2-yl)cyclohexyl]-N~2~-[(1H-indol-2-yl)methyl]glycinamide


Mass: 401.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 35% PEG 3350, 0.2M CaAC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 12410 / % possible obs: 96.7 % / Redundancy: 14.4 % / Biso Wilson estimate: 44.42 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.014 / Rrim(I) all: 0.052 / Χ2: 0.816 / Net I/σ(I): 9.2 / Num. measured all: 179104
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-214.10.9756130.8560.2671.0120.407100
2-2.0415.30.7786210.9170.2040.8050.419100
2.04-2.0816.20.6036100.9530.1530.6230.44599.8
2.08-2.1215.90.5436390.9530.1390.5610.451100
2.12-2.1716.10.4315970.9810.110.4450.45100
2.17-2.2215.60.3546210.9810.0910.3660.47399.8
2.22-2.275.80.2713820.920.0920.2880.96961
2.27-2.3414.30.2436180.9910.0660.2520.50698.9
2.34-2.4150.1856240.9920.0490.1910.518100
2.4-2.4814.20.1656270.9940.0450.1710.533100
2.48-2.5713.90.1256300.9950.0340.130.571100
2.57-2.6715.90.1066360.9980.0270.110.616100
2.67-2.816.10.0836260.9980.0210.0860.674100
2.8-2.9415.30.0716350.9980.0190.0740.821100
2.94-3.13150.0556600.9980.0150.0570.95199.8
3.13-3.3714.20.0466490.9990.0130.0481.21799.1
3.37-3.7111.50.0415330.9990.0120.0431.46182.4
3.71-4.2413.70.0376270.9990.010.0391.57795
4.24-5.35140.03368110.0090.0341.6799
5.35-5013.20.03378110.0090.0341.92599.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.08 Å39.49 Å
Translation5.08 Å39.49 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.8.3phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6wzz

6wzz


Resolution: 1.97→39.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.246 600 4.86 %RANDOM
Rwork0.206 ---
obs0.208 12336 96.8 %-
Displacement parametersBiso max: 125.12 Å2 / Biso mean: 51.01 Å2 / Biso min: 29.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.1076 Å20 Å20 Å2
2--1.1076 Å20 Å2
3----2.2152 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 1.97→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 30 39 1334
Biso mean--50.92 50.41 -
Num. residues----159
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d422SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes253HARMONIC5
X-RAY DIFFRACTIONt_it1347HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion163SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1440SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1347HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1833HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion15.85
LS refinement shellResolution: 1.97→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.2769 25 6.07 %
Rwork0.2219 387 -
all0.225 412 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -6.4701 Å / Origin y: 7.6964 Å / Origin z: 13.299 Å
111213212223313233
T-0.06 Å2-0.0191 Å2-0.0613 Å2--0.1872 Å20.023 Å2---0.0667 Å2
L2.2576 °2-0.59 °2-0.6263 °2-3.647 °20.7843 °2--3.1658 °2
S-0.0677 Å °0.2323 Å °0.2758 Å °0.0263 Å °0.0002 Å °-0.0579 Å °-0.1746 Å °-0.0682 Å °0.0675 Å °
Refinement TLS groupSelection details: { A|* }

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