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- PDB-8pry: Crystal structure of Trypanosoma cruzi glycerol kinase -

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Basic information

Entry
Database: PDB / ID: 8pry
TitleCrystal structure of Trypanosoma cruzi glycerol kinase
Componentsglycerol kinase
KeywordsTRANSFERASE / Glycerol metabolism / Trypanosoma cruzi / Glycosomes.
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. / Glycerol kinase / 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
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLipinski, O. / Sonani, R.R. / Dubin, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2020/39/B/NZ1/01551 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease.
Authors: Lipinski, O. / Sonani, R.R. / Dubin, G.
History
DepositionJul 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycerol kinase
B: glycerol kinase
C: glycerol kinase
D: glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,4498
Polymers233,0814
Non-polymers3684
Water7,260403
1
A: glycerol kinase
D: glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7254
Polymers116,5402
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-17 kcal/mol
Surface area37830 Å2
2
B: glycerol kinase
hetero molecules

C: glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7254
Polymers116,5402
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3800 Å2
ΔGint-22 kcal/mol
Surface area37030 Å2
Unit cell
Length a, b, c (Å)68.779, 89.321, 97.155
Angle α, β, γ (deg.)117.35, 88.99, 93.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
glycerol kinase


Mass: 58270.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_2g784 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2W444
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% w/v Polyethylene glycol 3350, 200 mM Magnesium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.07→44.61 Å / Num. obs: 117172 / % possible obs: 93.84 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 5.6
Reflection shellResolution: 2.07→2.11 Å / Num. unique obs: 4908 / CC1/2: 0.518

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→44.61 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 17.018 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23753 5822 5 %RANDOM
Rwork0.17598 ---
obs0.17899 111348 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.092 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.71 Å2-0.18 Å2
2---0.6 Å20.9 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.07→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15975 0 0 403 16378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01216283
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615284
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.63722004
X-RAY DIFFRACTIONr_angle_other_deg0.7761.5635534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.37652038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.6275112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.397102904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.22492
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023252
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_it3.6722.5958171
X-RAY DIFFRACTIONr_mcbond_other3.6672.5958171
X-RAY DIFFRACTIONr_mcangle_it4.9813.87910200
X-RAY DIFFRACTIONr_mcangle_other4.9813.8810201
X-RAY DIFFRACTIONr_scbond_it4.7252.9378112
X-RAY DIFFRACTIONr_scbond_other4.7252.9378113
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4514.24611805
X-RAY DIFFRACTIONr_long_range_B_refined8.01734.12217945
X-RAY DIFFRACTIONr_long_range_B_other8.01134.02917863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 404 -
Rwork0.352 7046 -
obs--81.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9222-0.2662-0.0750.99810.28271.1929-0.02950.14280.0614-0.1332-0.0193-0.0554-0.12560.04940.04880.1703-0.00750.01760.0615-0.03640.07822.8866-0.0012.5689
20.51570.35230.14441.35250.28260.79670.0827-0.0212-0.01170.1771-0.0698-0.0850.03290.031-0.01280.1479-0.0180.02950.0247-0.03580.09861.72068.175447.7576
31.4830.7511-0.26081.4675-0.27590.83490.0326-0.05860.00160.058-0.0189-0.0778-0.02730.0663-0.01360.1514-0.0296-0.01070.0412-0.05510.106333.432-30.366348.671
40.8046-0.4159-0.09812.0063-0.53380.8349-0.0436-0.1104-0.12480.0897-0.0338-0.11790.02580.06290.07740.20660.00160.02670.2197-0.05030.178637.6939-48.9774.4418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 601
2X-RAY DIFFRACTION2B1 - 601
3X-RAY DIFFRACTION3C1 - 601
4X-RAY DIFFRACTION4D1 - 601

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