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- PDB-2q2r: Trypanosoma cruzi glucokinase in complex with beta-D-glucose and ADP -

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Basic information

Entry
Database: PDB / ID: 2q2r
TitleTrypanosoma cruzi glucokinase in complex with beta-D-glucose and ADP
ComponentsGlucokinase 1, putative
KeywordsTRANSFERASE / ATPase hexose kinase family
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
ADENOSINE-5'-DIPHOSPHATE / beta-D-glucopyranose / Glucokinase 1, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCordeiro, A.T. / Caceres, A.J. / Vertommen, D. / Concepcion, J.L. / Michels, P.A. / Versees, W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of Trypanosoma cruzi Glucokinase Reveals Features Determining Oligomerization and Anomer Specificity of Hexose-phosphorylating Enzymes.
Authors: Cordeiro, A.T. / Caceres, A.J. / Vertommen, D. / Concepcion, J.L. / Michels, P.A. / Versees, W.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 21, 2024Group: 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_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

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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)83,4376
Polymers82,2232
Non-polymers1,2154
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-23 kcal/mol
Surface area28750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.937, 125.697, 65.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALASERSER5AA-5 - 3671 - 373
21ALAALASERSER5BB-5 - 3671 - 373
12BGCBGCADPADP2AC - D1001 - 2001
22BGCBGCADPADP2BE - F1001 - 2001

NCS ensembles :
ID
1
2

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Components

#1: Protein Glucokinase 1, putative


Mass: 41111.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053510187.100 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4E4E1, glucokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350 0.4 M di-ammonium hydrogen citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8140, 0.9776, 0.9769, 0.9732
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8141
20.97761
30.97691
40.97321
ReflectionResolution: 2.1→30 Å / Num. obs: 52608 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rsym value: 0.103 / Net I/σ(I): 18.1
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.898 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.494 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25809 2672 5.1 %RANDOM
Rwork0.19389 ---
obs0.19716 49734 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.062 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2--5.68 Å20 Å2
3----3.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 78 486 6278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225944
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9838050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71723.721258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35915994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6931538
X-RAY DIFFRACTIONr_chiral_restr0.1140.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024490
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.23048
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.24058
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2527
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7071.53762
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.56725888
X-RAY DIFFRACTIONr_scbond_it4.25432453
X-RAY DIFFRACTIONr_scangle_it5.6574.52162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11484medium positional0.150.5
239medium positional0.230.5
11382loose positional0.395
11484medium thermal1.962
239medium thermal3.612
11382loose thermal3.0210
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 197 -
Rwork0.287 3573 -
obs--99.95 %

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