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

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Basic information

Entry
Database: PDB / ID: 5azi
TitleCrystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP
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 / 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
4-NITROPHENYL PHOSPHATE / glycerol kinase
Similarity search - Component
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
Water2,702150
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 area3670 Å2
ΔGint-18 kcal/mol
Surface area37930 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 area3710 Å2
ΔGint-18 kcal/mol
Surface area37830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.669, 120.253, 154.593
Angle α, β, γ (deg.)90.00, 89.96, 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.: 150 / 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: 52.53 %
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: Jul 14, 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: 2.45→50 Å / Num. obs: 86170 / % possible obs: 98.2 % / Observed criterion σ(I): -1.5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1.29 / % possible all: 95.5

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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: 2.45→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 20.009 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.931 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 3632 5 %RANDOM
Rwork0.19552 ---
obs0.19872 68998 84.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.992 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.11 Å2
2---0.45 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15812 0 52 150 16014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215550
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.95721911
X-RAY DIFFRACTIONr_angle_other_deg0.798335755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60152050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0523.006652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.521152799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.11515128
X-RAY DIFFRACTIONr_chiral_restr0.0750.22462
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023686
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: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 102 -
Rwork0.237 1884 -
obs--32.15 %
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)
10.35440.3067-0.21860.5612-0.37360.88790.02620.01090.0459-0.1221-0.03070.0750.1361-0.04370.00450.12510.0736-0.03470.0866-0.0430.0326Chain A29.96171.186255.341
20.87540.47050.3930.41950.13840.9642-0.02660.1626-0.0056-0.03490.0488-0.0166-0.14540.1661-0.02210.04730.02950.01460.16030.020.0057Chain B65.512950.911359.5653
30.3577-0.30780.20950.5043-0.42420.91810.0287-0.0033-0.04220.1251-0.02910.0827-0.1316-0.03610.00040.1351-0.0740.03740.0835-0.03610.0359Chain C-1.9044-28.220321.957
40.9021-0.4822-0.40920.49170.17850.8556-0.0257-0.16690.00420.04880.0496-0.00740.1470.1735-0.02390.055-0.0293-0.01460.170.01930.0051Chain D33.6596-77.933417.7587
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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