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- PDB-6j9v: Crystal structure of Trypanosoma brucei gambiense glycerol kinase... -

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Basic information

Entry
Database: PDB / ID: 6j9v
TitleCrystal structure of Trypanosoma brucei gambiense glycerol kinase complex with ADP.
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, 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 ...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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / glycerol kinase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBalogun, E.O. / Chishima, T. / Ichinose, M. / Inaoka, D.K. / Kido, Y. / Ibrahim, B. / de Koning, H. / McKerrow, J.H. / Watanabe, Y. / Nozaki, T. ...Balogun, E.O. / Chishima, T. / Ichinose, M. / Inaoka, D.K. / Kido, Y. / Ibrahim, B. / 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: Reaction mechanism of the reverse reaction of African human trypanosomes glycerol kinase.
Authors: Balogun, E.O. / Chishima, T. / Ichinose, M. / Inaoka, D.K. / Kido, W. / Ibrahim, B. / de Koning, H. / McKerrow, J.H. / Watanabe, Y. / Nozaki, T. / Michels, P.A.M. / Harada, S. / Kita, K. / Shiba, T.
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)115,2607
Polymers114,1292
Non-polymers1,1315
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-24 kcal/mol
Surface area38050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.416, 120.948, 154.097
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 51.73 %
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: Dec 14, 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: 2.4→50 Å / Num. obs: 46371 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.71
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14037 / % possible all: 99

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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: 2.4→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.312 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.265 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25416 2339 5.1 %RANDOM
Rwork0.19346 ---
obs0.19653 43871 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2---0.3 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 72 7 7993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198151
X-RAY DIFFRACTIONr_bond_other_d0.0020.027802
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.96311035
X-RAY DIFFRACTIONr_angle_other_deg1.055317942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15451024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41722.988328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.831151402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3271564
X-RAY DIFFRACTIONr_chiral_restr0.0960.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219102
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021860
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_it5.4966.9874102
X-RAY DIFFRACTIONr_mcbond_other5.4866.9864101
X-RAY DIFFRACTIONr_mcangle_it7.36210.485124
X-RAY DIFFRACTIONr_mcangle_other7.36110.4815125
X-RAY DIFFRACTIONr_scbond_it6.3257.6614049
X-RAY DIFFRACTIONr_scbond_other6.3257.6614049
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.00811.2395912
X-RAY DIFFRACTIONr_long_range_B_refined11.01956.5598949
X-RAY DIFFRACTIONr_long_range_B_other11.01956.568950
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 156 -
Rwork0.29 3082 -
obs--98.3 %

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