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- PDB-8y1t: CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GAMBIENSE GLYCEROL KINASE... -

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Basic information

Entry
Database: PDB / ID: 8y1t
TitleCRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GAMBIENSE GLYCEROL KINASE COMPLEX WITH ADP and G3P
ComponentsGlycerol kinase
KeywordsTRANSFERASE / African trypanosomes / ATP synthesis / Drug target / 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, metazoa / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / SN-GLYCEROL-3-PHOSPHATE / glycerol kinase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBalogun, E.O. / Inaoka, D.K. / Ichinose, M. / Chishima, T. / Harada, S. / Kita, K. / Shiba, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)K43TW012015 United States
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GAMBIENSE GLYCEROL KINASE COMPLEX WITH ADP and G3P
Authors: Balogun, E.O. / Inaoka, D.K. / Ichinose, M. / Chishima, T. / Harada, S. / Kita, K. / Shiba, T.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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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)115,3648
Polymers114,1292
Non-polymers1,2356
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-37 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.563, 121.741, 154.278
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 / Production host: Escherichia coli (E. coli) / References: UniProt: D3KVM3, glycerol kinase
#2: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8-18% PEG 400, 0.1M HEPES, 11% 1,6-HEXANEDIOL, PH 7.5

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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: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45369 / % possible obs: 99.8 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.5
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2 / Num. unique obs: 14161 / CC1/2: 0.842 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9V

6j9v


Resolution: 2.4→19.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.016 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24982 2326 5 %RANDOM
Rwork0.19226 ---
obs0.19518 44323 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.455 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0 Å2
2---0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7912 0 77 0 7989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198141
X-RAY DIFFRACTIONr_bond_other_d0.0020.027793
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.96411024
X-RAY DIFFRACTIONr_angle_other_deg1.002317923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02151024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49423.006326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.103151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0911564
X-RAY DIFFRACTIONr_chiral_restr0.0860.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219088
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021850
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_it4.5157.0454102
X-RAY DIFFRACTIONr_mcbond_other4.5157.0444101
X-RAY DIFFRACTIONr_mcangle_it6.2910.5675124
X-RAY DIFFRACTIONr_mcangle_other6.28910.5685125
X-RAY DIFFRACTIONr_scbond_it5.1297.6674039
X-RAY DIFFRACTIONr_scbond_other5.1297.6674040
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.62611.275901
X-RAY DIFFRACTIONr_long_range_B_refined9.94756.5868840
X-RAY DIFFRACTIONr_long_range_B_other9.94756.5878841
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 157 -
Rwork0.306 3142 -
obs--99.64 %

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