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- PDB-5brd: Crystal structure of Trypanosoma cruzi glucokinase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5brd
TitleCrystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor BENZ-GlcN
ComponentsGlucokinase 1, putative
KeywordsTransferase/Transferase Inhibitor / Transferase / Hexose Kinase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding
Similarity search - Function
Glucokinase / Glucokinase / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(benzoylamino)-2-deoxy-beta-D-glucopyranose / Glucokinase 1, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsD'Antonio, E.L. / Perry, K. / Deinema, M.S. / Kearns, S.P. / Frey, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103499 United States
University of South Carolina Office of the Vice President for Research United States
CitationJournal: Mol.Biochem.Parasitol. / Year: 2016
Title: Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase.
Authors: D'Antonio, E.L. / Deinema, M.S. / Kearns, S.P. / Frey, T.A. / Tanghe, S. / Perry, K. / Roy, T.A. / Gracz, H.S. / Rodriguez, A. / D'Antonio, J.
History
DepositionMay 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Jul 20, 2016Group: Data collection
Revision 1.5Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations / Refinement description
Category: diffrn_detector / pdbx_audit_support ...diffrn_detector / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_detector.detector / _pdbx_audit_support.funding_organization ..._diffrn_detector.detector / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Glucokinase 1, putative
B: Glucokinase 1, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0204
Polymers84,4532
Non-polymers5672
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-34 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.567, 78.837, 76.605
Angle α, β, γ (deg.)90.000, 94.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucokinase 1, putative


Mass: 42226.648 Da / Num. of mol.: 2 / Fragment: UNP residues 1-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053510187.100 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4E4E1, glucokinase
#2: Sugar ChemComp-BG8 / 2-(benzoylamino)-2-deoxy-beta-D-glucopyranose / N-benzoyl-beta-D-glucosamine / 2-(benzoylamino)-2-deoxy-beta-D-glucose / 2-(benzoylamino)-2-deoxy-D-glucose / 2-(benzoylamino)-2-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 283.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: A glucose-free TcGlcK crystal was soaked in 1.0 mM BENZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 20% (w/v) PEG 3,350 for 28 hours

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Feb 15, 2015 / Details: ADSC HF-4M PIXEL ARRAY DETECTOR
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→76.37 Å / Num. obs: 31494 / % possible obs: 98.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 51.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.041 / Net I/σ(I): 12.9 / Num. measured all: 136171
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.493.70.8221.41147730760.5920.45492
8.98-76.374.40.03144.728106400.9990.01698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q2R

2q2r


Resolution: 2.4→49.056 Å / FOM work R set: 0.785 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1526 5.06 %
Rwork0.1929 56760 -
obs0.1961 28819 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.01 Å2 / Biso mean: 42.51 Å2 / Biso min: 5.34 Å2
Refinement stepCycle: final / Resolution: 2.4→49.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5696 0 40 87 5823
Biso mean--30.68 32.31 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085858
X-RAY DIFFRACTIONf_angle_d1.1727920
X-RAY DIFFRACTIONf_chiral_restr0.074870
X-RAY DIFFRACTIONf_plane_restr0.0051032
X-RAY DIFFRACTIONf_dihedral_angle_d15.7632188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.43760.39961050.31142171227679
2.4376-2.47750.3541510.2982415256690
2.4775-2.52020.30441060.27822549265596
2.5202-2.56610.32611180.26862647276596
2.5661-2.61540.33671620.25052683284598
2.6154-2.66880.33631380.25282583272197
2.6688-2.72680.32491220.25132668279097
2.7268-2.79020.32411380.25882578271698
2.7902-2.860.32441330.25432649278297
2.86-2.93730.31681540.24352575272997
2.9373-3.02380.3141440.22412628277297
3.0238-3.12130.28751340.21472584271895
3.1213-3.23290.28221350.22862650278598
3.2329-3.36230.29481510.21972589274098
3.3623-3.51530.28871560.20362654281098
3.5153-3.70060.29281080.1842601270996
3.7006-3.93230.25871450.18492635278097
3.9323-4.23580.23181410.17222593273497
4.2358-4.66170.20641420.15032512265493
4.6617-5.33560.23671370.16222614275197
5.3356-6.71950.24051450.1792616276197
6.7195-49.06640.16791580.13572566272495

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