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- PDB-6jaf: Crystal structure of Trypanosoma brucei gambiense glycerol kinase... -

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Basic information

Entry
Database: PDB / ID: 6jaf
TitleCrystal structure of Trypanosoma brucei gambiense glycerol kinase complex with PPi (pyrophosphatase reaction)
ComponentsGlycerol kinase
KeywordsTRANSFERASE / TRYPANOSOMA / GLYCEROL KINASE / SUGAR KINASE SUPERFAMILY / GLYCOSOME
Function / homology
Function and homology information


glycerol-3-phosphate biosynthetic process / glycerol kinase / glycerol kinase activity / glycerol catabolic process / triglyceride metabolic process / mitochondrion / ATP binding
Similarity search - Function
Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / glycerol kinase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBalogun, E.O. / Chishima, T. / Ichinose, M. / Inaoka, D.K. / Kido, Y. / Ibrahim, B. / Bringaud, F. / de Koning, H. / McKerrow, J.H. / Watanabe, Y. ...Balogun, E.O. / Chishima, T. / Ichinose, M. / Inaoka, D.K. / Kido, Y. / Ibrahim, B. / Bringaud, F. / de Koning, H. / McKerrow, J.H. / Watanabe, Y. / Nozaki, T. / Michels, P.A.M. / Harada, S. / Kita, K. / Shiba, T.
CitationJournal: To Be Published
Title: Glycerol Kinase of African Human Trypanosomes Possesses a Pyrophosphatase Activity.
Authors: Balogun, E.O.
History
DepositionJan 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Glycerol kinase
B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4895
Polymers114,1292
Non-polymers3603
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-17 kcal/mol
Surface area37940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.055, 120.461, 154.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycerol kinase


Mass: 57064.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote)
Gene: gk / Plasmid: PET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3+PRARE2) / References: UniProt: D3KVM3, glycerol kinase
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 8-18% PEG 400, 0.1M HEPES, 11% 1,6-HEXANEDIOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26892 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.95
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8073

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXL

3wxl


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.885 / SU B: 20.392 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29779 1347 5 %RANDOM
Rwork0.21367 ---
obs0.21792 25392 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-0 Å2
2---0.25 Å20 Å2
3---0.52 Å2
Refinement stepCycle: 1 / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 21 0 7935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198096
X-RAY DIFFRACTIONr_bond_other_d0.0020.027776
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.95510953
X-RAY DIFFRACTIONr_angle_other_deg0.943317880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81551024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2622.988328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.208151402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4621564
X-RAY DIFFRACTIONr_chiral_restr0.0690.21230
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219076
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021848
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7658.4834102
X-RAY DIFFRACTIONr_mcbond_other3.7648.4824101
X-RAY DIFFRACTIONr_mcangle_it5.94212.7225124
X-RAY DIFFRACTIONr_mcangle_other5.94212.7235125
X-RAY DIFFRACTIONr_scbond_it3.6858.8783994
X-RAY DIFFRACTIONr_scbond_other3.6858.8783994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.90113.1625830
X-RAY DIFFRACTIONr_long_range_B_refined8.50867.4148955
X-RAY DIFFRACTIONr_long_range_B_other8.50767.4138955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 87 -
Rwork0.29 1812 -
obs--99.89 %

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