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- PDB-5gn5: Crystal structure of glycerol kinase from Trypanosoma brucei gamb... -

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Basic information

Entry
Database: PDB / ID: 5gn5
TitleCrystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with cumarin derivative-17
ComponentsGlycerol kinase
KeywordsTRANSFERASE / Glycerol kinase / inhibitor / drug / African trypanosomes
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
Chem-6XZ / glycerol kinase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBalogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. ...Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, T. / May, B. / Sato, T. / Kido, Y. / Takeshi, N. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. / Moore, A.L. / Harada, S. / Kita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japanese Society for the Promotion of Science26253025 Japan
CitationJournal: Faseb J. / Year: 2019
Title: Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase ofTrypanosoma brucei brucei.
Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y. ...Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tsuge, C. / May, B. / Sato, T. / Kido, Y. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Watanabe, Y.I. / Moore, A.L. / Harada, S. / Kita, K.
History
DepositionJul 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.name
Revision 1.3Nov 8, 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

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)228,32312
Polymers226,4254
Non-polymers1,8988
Water3,567198
1
A: Glycerol kinase
B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1616
Polymers113,2122
Non-polymers9494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-17 kcal/mol
Surface area37710 Å2
MethodPISA
2
C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1616
Polymers113,2122
Non-polymers9494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-19 kcal/mol
Surface area37740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.030, 63.205, 154.848
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycerol kinase


Mass: 56606.125 Da / Num. of mol.: 4
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-6XZ / 4-[[4-(4-methoxyphenyl)piperazin-1-yl]methyl]-7,8-bis(oxidanyl)chromen-2-one


Mass: 382.410 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22N2O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 28, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 56927 / % possible obs: 97.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.35 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXI

3wxi


Resolution: 2.85→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.864 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.508 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28629 2454 5 %RANDOM
Rwork0.19415 ---
obs0.19881 46711 88.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0.08 Å2
2---2.72 Å2-0 Å2
3---2.94 Å2
Refinement stepCycle: 1 / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15804 0 136 198 16138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01916272
X-RAY DIFFRACTIONr_bond_other_d0.0030.0215620
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.96322020
X-RAY DIFFRACTIONr_angle_other_deg1.1613.00235916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.07752048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08123.006652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.063152800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.56515128
X-RAY DIFFRACTIONr_chiral_restr0.0970.22460
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023704
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_it1.7743.6858204
X-RAY DIFFRACTIONr_mcbond_other1.7743.6858203
X-RAY DIFFRACTIONr_mcangle_it3.0595.52310248
X-RAY DIFFRACTIONr_mcangle_other3.0595.52310249
X-RAY DIFFRACTIONr_scbond_it1.6183.9528068
X-RAY DIFFRACTIONr_scbond_other1.6183.9528068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8345.84711773
X-RAY DIFFRACTIONr_long_range_B_refined5.76730.01318336
X-RAY DIFFRACTIONr_long_range_B_other5.76730.01118334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 115 -
Rwork0.279 2245 -
obs--59.72 %
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)
10.536-0.29980.17170.2124-0.14421.0096-0.05010.1347-0.09010.0402-0.00560.0536-0.00850.12560.05570.1668-0.08250.03760.2158-0.01250.054245.55680.546716.7464
20.6366-0.4743-0.26140.7470.19071.03540.08880.23150.0848-0.0611-0.0403-0.0946-0.0735-0.335-0.04850.1642-0.0385-0.0180.31650.05750.0236-4.662835.260420.7478
30.53280.3111-0.25090.2289-0.13010.967-0.0654-0.12090.0853-0.04640.01380.05590.01240.13720.05160.16920.0838-0.02880.2181-0.010.0487106.0763.957560.6613
40.54590.42010.26330.70620.22831.06260.0868-0.2095-0.08250.0548-0.0497-0.10840.0885-0.3388-0.03710.15980.04080.0210.31090.05350.028355.8194-30.725456.6529
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 511
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B-1 - 511
4X-RAY DIFFRACTION2B601
5X-RAY DIFFRACTION3C-1 - 511
6X-RAY DIFFRACTION3C601
7X-RAY DIFFRACTION4D-1 - 511
8X-RAY DIFFRACTION4D601

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