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- PDB-6edi: Crystal structure of Leishmania braziliensis glucokinase -

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Basic information

Entry
Database: PDB / ID: 6edi
TitleCrystal structure of Leishmania braziliensis glucokinase
ComponentsGlucokinase
KeywordsTRANSFERASE / open conformation / dimeric
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
Biological speciesLeishmania braziliensis MHOM/BR/75/M2904 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBuechner, G.S. / Millington, M.E. / Perry, K. / D'Antonio, E.L.
CitationJournal: Mol. Biochem. Parasitol. / Year: 2019
Title: The crystal structure of glucokinase from Leishmania braziliensis.
Authors: Buechner, G.S. / Millington, M.E. / Perry, K. / D'Antonio, E.L.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Glucokinase


Theoretical massNumber of molelcules
Total (without water)88,6392
Polymers88,6392
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-30 kcal/mol
Surface area30860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.477, 63.261, 85.570
Angle α, β, γ (deg.)90.000, 107.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucokinase / Glucokinase 1


Mass: 44319.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis MHOM/BR/75/M2904 (eukaryote)
Gene: LBRM_35_2550 / Plasmid: pET-28a(+) / Details (production host): kanamycin-resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4HPA0, glucokinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.06 Å3/Da / Density % sol: 40.41 % / Description: single crystal
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.0 uL 20.3 mg/mL LbGlcK in 50 mM HEPES, pH 7.5, 0.2 M imidazole, 2 mM magnesium chloride + 1.0 uL precipitant solution (26% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5) ...Details: 1.0 uL 20.3 mg/mL LbGlcK in 50 mM HEPES, pH 7.5, 0.2 M imidazole, 2 mM magnesium chloride + 1.0 uL precipitant solution (26% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5) equilibrated against 80 uL precipitant solution, 96-well sitting-drop plate (Innovadyne), 295 K
PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2016
RadiationMonochromator: cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.84→81.47 Å / Num. obs: 58585 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.062 / Rrim(I) all: 0.116 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.883.31.1741069532460.4380.7421.3931.188.5
9.03-81.473.50.06819875610.9950.0410.0836.899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.17data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q2R

2q2r


Resolution: 1.85→49.966 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.46
RfactorNum. reflection% reflection
Rfree0.2618 2955 5.08 %
Rwork0.2124 --
obs0.2149 58205 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 35.11 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 1.85→49.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 0 176 6126
Biso mean---35.17 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076066
X-RAY DIFFRACTIONf_angle_d1.1818212
X-RAY DIFFRACTIONf_chiral_restr0.072930
X-RAY DIFFRACTIONf_plane_restr0.0051054
X-RAY DIFFRACTIONf_dihedral_angle_d15.3122176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.88040.35391410.30462537267896
1.8804-1.91280.30881260.27912637276397
1.9128-1.94760.30921320.26622609274197
1.9476-1.9850.28051250.25562630275598
1.985-2.02560.33951220.25582638276097
2.0256-2.06960.29981570.25112572272997
2.0696-2.11780.30851470.23782611275897
2.1178-2.17070.25711410.23092581272296
2.1707-2.22940.30611370.22322567270496
2.2294-2.2950.28551450.23712633277898
2.295-2.36910.28061490.23722649279898
2.3691-2.45380.29061350.2312629276499
2.4538-2.5520.30821370.22972654279198
2.552-2.66810.29641560.22712604276098
2.6681-2.80880.32331350.23682609274497
2.8088-2.98470.3071630.23922636279998
2.9847-3.21520.25641480.2232662281099
3.2152-3.53860.27971420.20712677281999
3.5386-4.05050.22691650.18912661282698
4.0505-5.10240.20571230.17092681280497
5.1024-49.98460.20531290.18642773290298

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