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- PDB-9lyy: Crystal structure of glycerol kinase from Entamoeba histolytica c... -

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Basic information

Entry
Database: PDB / ID: 9lyy
TitleCrystal structure of glycerol kinase from Entamoeba histolytica complexed with ADP and G3P.
Componentsglycerol kinase
KeywordsTRANSFERASE / GLYCEROL METABOLISM / Entamoeba histolytica / TRANSFERAS
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
FGGY family of carbohydrate kinases signature 1. / 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 speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBalogun, E.O. / Jeelani, G. / Hane, E. / Kondo, H. / Hasegawa, Y. / Kojima, C. / Chishima, T. / Harada, S. / Kishikawa, J. / Nozaki, T. / Shiba, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural insights into the reverse reaction mechanism of glycerol kinase from Entamoeba histolytica
Authors: Balogun, E.O. / Jeelani, G. / Hane, E. / Kondo, H. / Hasegawa, Y. / Kojima, C. / Chishima, T. / Harada, S. / Kishikawa, J. / Nozaki, T. / Shiba, T.
History
DepositionFeb 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2026Provider: 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)109,2249
Polymers107,7832
Non-polymers1,4417
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-63 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.354, 79.948, 205.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein glycerol kinase / ATP:glycerol 3-phosphotransferase


Mass: 53891.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_164850 / Plasmid: pCOLD1 / Details (production host): pCOLD1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5K1V6Z1, glycerol kinase

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Non-polymers , 5 types, 273 molecules

#2: 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
#3: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20 % PEG3350, 0.2 M HCOONa, 50 mM Phosphate buffer (pH 6.8)
PH range: 6.5-7.0

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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: May 15, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 123531 / % possible obs: 98 % / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.083 / Net I/σ(I): 12.9
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 19433 / CC1/2: 0.903 / Rpim(I) all: 0.783 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.128 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20579 6103 4.9 %RANDOM
Rwork0.18566 ---
obs0.18665 117299 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.752 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7560 0 89 266 7915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197850
X-RAY DIFFRACTIONr_bond_other_d0.0020.027515
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9610636
X-RAY DIFFRACTIONr_angle_other_deg0.934317347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26425.399326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.348151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6231524
X-RAY DIFFRACTIONr_chiral_restr0.0830.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028801
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021717
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_it1.4282.7883920
X-RAY DIFFRACTIONr_mcbond_other1.4282.7883919
X-RAY DIFFRACTIONr_mcangle_it2.1534.1794907
X-RAY DIFFRACTIONr_mcangle_other2.1534.1794908
X-RAY DIFFRACTIONr_scbond_it2.1773.1033930
X-RAY DIFFRACTIONr_scbond_other2.1773.1033930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4674.5275730
X-RAY DIFFRACTIONr_long_range_B_refined4.50222.4648873
X-RAY DIFFRACTIONr_long_range_B_other4.48722.3778790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.637 Å
RfactorNum. reflection% reflection
Rfree0.318 441 -
Rwork0.327 8357 -
obs--96.08 %

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