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

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Basic information

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


organelle / glucokinase / glucokinase activity / 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
Chem-4UZ / Glucokinase 1, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 1.4Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Dec 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Glucokinase 1, putative
B: Glucokinase 1, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0804
Polymers84,4532
Non-polymers6272
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-39 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.673, 79.047, 76.445
Angle α, β, γ (deg.)90.000, 94.740, 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-4UZ / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-beta-D-glucopyranose / N-[(benzyloxy)carbonyl]-beta-D-glucosamine / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-beta-D-glucose / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-D-glucose / 2-{[(benzyloxy)carbonyl]amino}-2-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 313.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19NO7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 51.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: A glucose-free TcGlcK crystal was soaked in 1.0 mM CBZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 15% (w/v) PEG 3,350 for 24 hours

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2014 / Details: LR-Design detector positioner
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 28549 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 52.98 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.062 / Rrim(I) all: 0.119 / Χ2: 1.122 / Net I/av σ(I): 13.262 / Net I/σ(I): 9.8 / Num. measured all: 105473
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.70.69428430.6740.4220.8141.042100
2.59-2.693.70.53828390.7510.3260.631.153100
2.69-2.823.70.41228360.8390.2490.4831.152100
2.82-2.963.70.28428520.9230.1710.3321.223100
2.96-3.153.70.19928390.9580.120.2321.151100
3.15-3.393.70.13828400.9740.0830.1611.16100
3.39-3.733.70.10328570.9820.0620.1211.108100
3.73-4.273.70.08528780.9860.0510.0991.021100
4.27-5.383.70.08328610.9840.0510.0971.106100
5.38-503.50.06129040.990.0390.0731.10198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q2R

2q2r


Resolution: 2.5→27.427 Å / FOM work R set: 0.7902 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 1434 5.06 %
Rwork0.1902 26898 -
obs0.1924 28332 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.44 Å2 / Biso mean: 78.49 Å2 / Biso min: 42.8 Å2
Refinement stepCycle: final / Resolution: 2.5→27.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5696 0 44 4 5744
Biso mean--73.29 60.4 -
Num. residues----734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095862
X-RAY DIFFRACTIONf_angle_d1.1247924
X-RAY DIFFRACTIONf_chiral_restr0.071870
X-RAY DIFFRACTIONf_plane_restr0.0051030
X-RAY DIFFRACTIONf_dihedral_angle_d14.942194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58930.32061610.272726502811100
2.5893-2.69290.31861360.250826912827100
2.6929-2.81530.31831330.245827062839100
2.8153-2.96360.30321500.231726502800100
2.9636-3.1490.29131260.240826952821100
3.149-3.39170.31471290.221826932822100
3.3917-3.73230.22481450.193526772822100
3.7323-4.27060.22261530.180327032856100
4.2706-5.37390.19611420.161626972839100
5.3739-27.42870.17171590.14982736289599

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