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

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Basic information

Entry
Database: PDB / ID: 5brf
TitleCrystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor HPOP-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
Chem-4V5 / Glucokinase 1, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 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: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / 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: Data collection / Database references ...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
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)85,1084
Polymers84,4532
Non-polymers6552
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-39 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.114, 80.016, 75.797
Angle α, β, γ (deg.)90.000, 95.050, 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: Trypanosoma cruzi glucokinase
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-4V5 / 2-deoxy-2-{[3-(4-hydroxyphenyl)propanoyl]amino}-alpha-D-glucopyranose / N-[3-(4-hydroxyphenyl)propanoyl]-alpha-D-glucosamine / 2-deoxy-2-{[3-(4-hydroxyphenyl)propanoyl]amino}-alpha-D-glucose / 2-deoxy-2-{[3-(4-hydroxyphenyl)propanoyl]amino}-D-glucose / 2-deoxy-2-{[3-(4-hydroxyphenyl)propanoyl]amino}-glucose


Type: D-saccharide, alpha linking / Mass: 327.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21NO7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: A glucose-free TcGlcK crystal was soaked in 1.0 mM HPOP-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 18% (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-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46434 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 44.35 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.039 / Rrim(I) all: 0.078 / Χ2: 1.11 / Net I/av σ(I): 18.963 / Net I/σ(I): 8.2 / Num. measured all: 162758
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.183.20.38945470.7920.2420.460.95297.4
2.18-2.263.30.30545700.8830.1870.3591.11297.8
2.26-2.373.30.24445870.9070.150.2881.16897.7
2.37-2.493.60.19946690.9380.1170.2321.14899.3
2.49-2.653.60.16446400.9570.0970.1911.1999.2
2.65-2.853.40.13846130.9660.0830.1621.17398
2.85-3.143.70.11146810.9790.0640.1281.1899.3
3.14-3.593.60.08546980.9870.0490.0981.06599
3.59-4.523.70.06446670.9920.0360.0741.0899.1
4.52-503.60.03747620.9970.0220.0431.02598.6

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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: 2.102→48.395 Å / FOM work R set: 0.8157 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 2342 5.05 %
Rwork0.1905 44065 -
obs0.1928 46407 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.99 Å2 / Biso mean: 42.18 Å2 / Biso min: 16.7 Å2
Refinement stepCycle: final / Resolution: 2.102→48.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5654 0 46 244 5944
Biso mean--37.68 39.92 -
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085820
X-RAY DIFFRACTIONf_angle_d1.0877868
X-RAY DIFFRACTIONf_chiral_restr0.074866
X-RAY DIFFRACTIONf_plane_restr0.0051022
X-RAY DIFFRACTIONf_dihedral_angle_d14.2172170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.102-2.1450.31351120.23862382249490
2.145-2.19170.25351330.23122561269498
2.1917-2.24260.25311130.22712597271098
2.2426-2.29870.27351280.22592563269197
2.2987-2.36090.30941670.22392567273498
2.3609-2.43030.29611330.22242618275199
2.4303-2.50880.28141560.21412583273999
2.5088-2.59850.30441520.22232590274299
2.5985-2.70250.30221440.22352610275499
2.7025-2.82550.26911370.21782567270498
2.8255-2.97440.26061380.21272610274899
2.9744-3.16070.26711460.21472629277599
3.1607-3.40470.26911380.20622628276699
3.4047-3.74720.23441260.18642586271298
3.7472-4.28920.1891580.171326412799100
4.2892-5.40280.19031210.16022651277299
5.4028-48.40810.20721400.16412682282298

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