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- PDB-6teq: Crystal structure of a galactokinase from Bifidobacterium infanti... -

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Basic information

Entry
Database: PDB / ID: 6teq
TitleCrystal structure of a galactokinase from Bifidobacterium infantis in complex with 2-deoxy-2-fluoro-galactose
ComponentsGalactokinase
KeywordsTRANSFERASE / 2FGal / complex / galactokinase
Function / homology
Function and homology information


L-arabinokinase activity / galactokinase / galactokinase activity / galactose metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal ...Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-deoxy-2-fluoro-beta-D-galactopyranose / 2-deoxy-2-fluoro-alpha-D-galactopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / galactokinase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKeenan, T. / Parmeggiani, F. / Fontenelle, C.Q. / Malassis, J. / Vendeville, J. / Offen, W.A. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. ...Keenan, T. / Parmeggiani, F. / Fontenelle, C.Q. / Malassis, J. / Vendeville, J. / Offen, W.A. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. / Young, C. / Charnock, S. / Davies, G.J. / Linclau, B. / Flitsch, S.L. / Fascione, M.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M02847X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M028836/1 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2020
Title: Profiling Substrate Promiscuity of Wild-Type Sugar Kinases for Multi-fluorinated Monosaccharides.
Authors: Keenan, T. / Parmeggiani, F. / Malassis, J. / Fontenelle, C.Q. / Vendeville, J.B. / Offen, W. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. / Young, C. / Charnock, S.J. / Davies, G.J. / ...Authors: Keenan, T. / Parmeggiani, F. / Malassis, J. / Fontenelle, C.Q. / Vendeville, J.B. / Offen, W. / Both, P. / Huang, K. / Marchesi, A. / Heyam, A. / Young, C. / Charnock, S.J. / Davies, G.J. / Linclau, B. / Flitsch, S.L. / Fascione, M.A.
History
DepositionNov 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 30, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first
Revision 1.4Jan 24, 2024Group: 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: Galactokinase
B: Galactokinase
C: Galactokinase
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,87556
Polymers183,2624
Non-polymers5,61452
Water28,3021571
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,20012
Polymers45,8151
Non-polymers1,38511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,01313
Polymers45,8151
Non-polymers1,19812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,93621
Polymers45,8151
Non-polymers2,12120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,72510
Polymers45,8151
Non-polymers9109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.218, 164.386, 115.874
Angle α, β, γ (deg.)90.000, 95.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Galactokinase /


Mass: 45815.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Galactokinase with C-terminal His-tag
Source: (gene. exp.) Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 (bacteria)
Gene: Blon_2062 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7GUI0

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Sugars , 2 types, 8 molecules

#5: Sugar
ChemComp-GAF / 2-deoxy-2-fluoro-alpha-D-galactopyranose / 2-DEOXY-2-FLUORO-GALACTOSE / 2-deoxy-2-fluoro-alpha-D-galactose / 2-deoxy-2-fluoro-D-galactose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar
ChemComp-2FG / 2-deoxy-2-fluoro-beta-D-galactopyranose / 2-FLUORO-2-DEOXY-BETA-D-GALACTOPYRANOSE / 2-deoxy-2-fluoro-beta-D-galactose / 2-deoxy-2-fluoro-D-galactose / 2-deoxy-2-fluoro-galactose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 1615 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1571 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.25 M NaCl and 22 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.44→94.55 Å / Num. obs: 349052 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 4.8
Reflection shellResolution: 1.44→1.46 Å / Rmerge(I) obs: 1.058 / Num. unique obs: 17309 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TEP

6tep


Resolution: 1.44→94.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.435 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 17586 5 %RANDOM
Rwork0.1687 ---
obs0.1704 331367 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.64 Å2 / Biso mean: 18.964 Å2 / Biso min: 3.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.85 Å2
2---1.39 Å2-0 Å2
3---1.36 Å2
Refinement stepCycle: final / Resolution: 1.44→94.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12441 0 364 1571 14376
Biso mean--29.09 31.01 -
Num. residues----1673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01313849
X-RAY DIFFRACTIONr_bond_other_d0.0070.01712767
X-RAY DIFFRACTIONr_angle_refined_deg1.861.64618816
X-RAY DIFFRACTIONr_angle_other_deg1.6531.58629677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88851853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11622.571704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01152184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91596
X-RAY DIFFRACTIONr_chiral_restr0.1070.21809
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216124
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022845
X-RAY DIFFRACTIONr_rigid_bond_restr4.591326614
LS refinement shellResolution: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 1370 -
Rwork0.283 24389 -
all-25759 -
obs--99.77 %

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