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

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Basic information

Entry
Database: PDB / ID: 9lzi
TitleCrystal structure of glycerol kinase from Entamoeba histolytica complexed with GK-butyl.
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
4-butyl-7,8-bis(oxidanyl)chromen-2-one / PHOSPHATE ION / glycerol kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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)108,71512
Polymers107,6412
Non-polymers1,07510
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-50 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.865, 204.260, 82.630
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 / ATP:glycerol 3-phosphotransferase


Mass: 53820.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CL6EHI_164850 / Plasmid: pCOLD1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5K1V6Z1, glycerol kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-6Y0 / 4-butyl-7,8-bis(oxidanyl)chromen-2-one


Mass: 234.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.81 %
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: Nov 18, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 78241 / % possible obs: 99.1 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.091 / Net I/σ(I): 13.5
Reflection shellResolution: 1.89→2.01 Å / Rmerge(I) obs: 1.156 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 12328 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→19.95 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.628 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22468 4020 5.1 %RANDOM
Rwork0.19325 ---
obs0.19492 74075 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.89→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7555 0 67 140 7762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197758
X-RAY DIFFRACTIONr_bond_other_d0.0020.027447
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.95510489
X-RAY DIFFRACTIONr_angle_other_deg0.9623.00117178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76125.399326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.299151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5571524
X-RAY DIFFRACTIONr_chiral_restr0.0880.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028694
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021694
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_it2.1773.8293882
X-RAY DIFFRACTIONr_mcbond_other2.1763.8293881
X-RAY DIFFRACTIONr_mcangle_it3.0945.7324849
X-RAY DIFFRACTIONr_mcangle_other3.0945.7334850
X-RAY DIFFRACTIONr_scbond_it2.9584.2483876
X-RAY DIFFRACTIONr_scbond_other2.9464.2483876
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6186.2075641
X-RAY DIFFRACTIONr_long_range_B_refined5.85130.6218654
X-RAY DIFFRACTIONr_long_range_B_other5.85330.6258655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 284 -
Rwork0.367 5278 -
obs--97.22 %

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