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

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Basic information

Entry
Database: PDB / ID: 5azj
TitleCrystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP (with disulfide bridge)
Components(Glycerol kinase) x 2
KeywordsTRANSFERASE / Glycerol kinase / Phosphatase / 4NP / 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
4-NITROPHENYL PHOSPHATE / glycerol kinase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsBalogun, E.O. / Inaoka, D.K. / Shiba, T. / Tokuoka, S.M. / Tokumasu, F. / Sakamoto, K. / Michels, P.A.M. / Harada, S. / Kita, K.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2017
Title: Glycerol kinase of African trypanosomes possesses an intrinsic phosphatase activity.
Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Tokuoka, S.M. / Tokumasu, F. / Sakamoto, K. / Kido, Y. / Michels, P.A.M. / Watanabe, Y.I. / Harada, S. / Kita, K.
History
DepositionOct 8, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)229,22510
Polymers228,4184
Non-polymers8076
Water1,838102
1
A: Glycerol kinase
B: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6135
Polymers114,2092
Non-polymers4033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-16 kcal/mol
Surface area38140 Å2
MethodPISA
2
C: Glycerol kinase
D: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6135
Polymers114,2092
Non-polymers4033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-14 kcal/mol
Surface area37980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.737, 120.031, 154.706
Angle α, β, γ (deg.)90.00, 90.02, 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote)
Gene: gk / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3+pRARE2) / References: UniProt: D3KVM3, glycerol kinase
#2: Protein Glycerol kinase


Mass: 57144.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote)
Gene: gk / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3+pRARE2) / References: UniProt: D3KVM3, glycerol kinase
#3: Chemical ChemComp-4NP / 4-NITROPHENYL PHOSPHATE


Mass: 219.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6NO6P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 18, 2015
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 70299 / Num. obs: 69743 / % possible obs: 99.2 % / Observed criterion σ(I): -1.5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.53 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXL

3wxl


Resolution: 2.61→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 24.232 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25703 3414 5.1 %RANDOM
Rwork0.19559 ---
obs0.19876 64172 95.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.036 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å20.03 Å2
2---0.46 Å2-0 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.61→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15812 0 52 102 15966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916186
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215548
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.95721902
X-RAY DIFFRACTIONr_angle_other_deg0.795335744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6352048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04623.006652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.218152798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.59815128
X-RAY DIFFRACTIONr_chiral_restr0.0730.22460
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023684
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.612→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 145 -
Rwork0.252 3138 -
obs--64.56 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.3357-0.3808-0.24570.61480.53861.11780.0507-0.02060.04720.1282-0.0568-0.08460.15420.06780.00610.2042-0.1054-0.03490.10720.04430.028Chain A33.773827.696921.957
21.0438-0.57760.6550.5537-0.2030.9677-0.0335-0.22180.00540.00510.0530.0059-0.1272-0.2176-0.01950.0938-0.03960.01640.2307-0.0290.0068Chain B-1.925677.315117.761
30.35190.37650.25450.6170.59441.10440.05160.0118-0.049-0.1352-0.0594-0.0876-0.14470.05680.00780.20670.10430.04350.10110.050.0366Chain C1.8925-1.574455.3973
41.00630.5199-0.70940.6344-0.2750.9608-0.03670.1968-0.004-0.03240.05360.01530.1295-0.2106-0.01690.09170.0429-0.01840.2307-0.02580.0062Chain D-33.8056-51.179759.6033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 511
2X-RAY DIFFRACTION2B-1 - 511
3X-RAY DIFFRACTION3C-1 - 511
4X-RAY DIFFRACTION4D-1 - 511

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