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- PDB-6j9q: Crystal structure of Trypanosoma brucei gambiense glycerol kinase... -

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Basic information

Entry
Database: PDB / ID: 6j9q
TitleCrystal structure of Trypanosoma brucei gambiense glycerol kinase complex with AMP-PNP.
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 / 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 ...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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / glycerol kinase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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, Y. / 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

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)230,83614
Polymers228,2594
Non-polymers2,57710
Water34219
1
A: Glycerol kinase
B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4187
Polymers114,1292
Non-polymers1,2895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-22 kcal/mol
Surface area38480 Å2
MethodPISA
2
C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4187
Polymers114,1292
Non-polymers1,2895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-18 kcal/mol
Surface area38550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.598, 123.149, 154.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycerol kinase


Mass: 57064.625 Da / Num. of mol.: 4
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 62097 / % possible obs: 98.4 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.068 / Net I/σ(I): 12.5
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique obs: 20049 / % possible all: 98

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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: 2.7→19.88 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.084 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26934 3237 5.1 %RANDOM
Rwork0.19093 ---
obs0.19492 60749 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.957 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å20.27 Å2
2---0.56 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.7→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15828 0 160 19 16007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916320
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215608
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.96422102
X-RAY DIFFRACTIONr_angle_other_deg0.971335892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90552048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55622.988656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.016152804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39715128
X-RAY DIFFRACTIONr_chiral_restr0.0770.22478
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023724
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_it3.8066.9318204
X-RAY DIFFRACTIONr_mcbond_other3.8066.938203
X-RAY DIFFRACTIONr_mcangle_it5.8810.39410248
X-RAY DIFFRACTIONr_mcangle_other5.8810.39410249
X-RAY DIFFRACTIONr_scbond_it3.7047.3298116
X-RAY DIFFRACTIONr_scbond_other3.7047.3298116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.91310.83711855
X-RAY DIFFRACTIONr_long_range_B_refined8.45155.06617677
X-RAY DIFFRACTIONr_long_range_B_other8.45155.06717678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 204 -
Rwork0.295 4341 -
obs--98.42 %

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