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- PDB-3wxi: Crystal structure of trypanosoma brucei gambiense glycerol kinase... -

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Basic information

Entry
Database: PDB / ID: 3wxi
TitleCrystal structure of trypanosoma brucei gambiense glycerol kinase (ligand-free form)
ComponentsGlycerol kinase
KeywordsTRANSFERASE / GLYCEROL KINASE / TRYPANOSOMA / SUGAR KINASE SUPERFAMILY / Glycosome
Function / homology
Function and homology information


glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol catabolic process / phosphorylation / 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
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBalogun, E.O. / Inaoka, D.K. / Shiba, T. / Kido, Y. / Tsuge, T. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. ...Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Kido, Y. / Tsuge, T. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A.M. / Kita, K. / Harada, S.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Molecular basis for the reverse reaction of African human trypanosomes glycerol kinase.
Authors: Balogun, E.O. / Inaoka, D.K. / Shiba, T. / Kido, Y. / Tsuge, C. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Michels, P.A. / Kita, K. / Harada, S.
History
DepositionAug 1, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerol kinase
B: Glycerol kinase


Theoretical massNumber of molelcules
Total (without water)114,1292
Polymers114,1292
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-19 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.763, 131.979, 148.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3+pRARE2) / References: UniProt: D3KVM3, glycerol kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 26, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 30649 / Num. obs: 29027 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.675 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W40

2w40


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 43.736 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28208 1539 5 %RANDOM
Rwork0.20183 ---
all0.21 30649 --
obs0.20596 29027 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.885 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å20 Å20 Å2
2--2.48 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7897 0 0 9 7906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228065
X-RAY DIFFRACTIONr_angle_refined_deg1.591.95310913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20651023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81822.997327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.938151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3771564
X-RAY DIFFRACTIONr_chiral_restr0.1040.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216001
X-RAY DIFFRACTIONr_mcbond_it0.6291.55079
X-RAY DIFFRACTIONr_mcangle_it1.19928155
X-RAY DIFFRACTIONr_scbond_it1.53632986
X-RAY DIFFRACTIONr_scangle_it2.6354.52758
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 115 -
Rwork0.31 2118 -
obs--99.51 %
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)
12.2058-1.35570.01891.978-0.19942.2629-0.4214-0.03130.06610.22210.06020.01050.3057-0.25790.36120.2257-0.17450.17340.3607-0.13940.3143-33.529415.895-15.4023
21.91510.528-1.22913.57990.35492.813-0.00520.41450.0977-0.86670.00740.78340.2296-0.3855-0.00220.3166-0.0039-0.21290.3799-0.02170.2258-1.459-38.568-20.924
31.17540.22841.49720.38510.76332.6232-0.1162-0.12210.2392-0.19030.0885-0.063-0.3416-0.03730.02770.2758-0.10760.00570.3383-0.12090.4107-20.976-16.129-24.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 511
2X-RAY DIFFRACTION2B-1 - 510
3X-RAY DIFFRACTION3A601 - 602
4X-RAY DIFFRACTION3B601 - 607

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