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

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Basic information

Entry
Database: PDB / ID: 6ter
TitleCrystal structure of a galactokinase from Bifidobacterium infantis in complex with Galactose
ComponentsGalactokinase
KeywordsTRANSFERASE / Gal / complex / galactokinase
Function / homology
Function and homology information


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
beta-D-galactopyranose / 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: 1.68 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, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M02847X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M028836/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M028941/1 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
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_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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)190,94479
Polymers183,2624
Non-polymers7,68275
Water13,763764
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,15230
Polymers45,8151
Non-polymers3,33729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,99523
Polymers45,8151
Non-polymers2,17922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,05215
Polymers45,8151
Non-polymers1,23714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,74411
Polymers45,8151
Non-polymers92910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.320, 164.929, 113.630
Angle α, β, γ (deg.)90.000, 94.970, 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, 6 molecules

#6: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 833 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.15 - 0.25 M NaCl and 18 - 22 % (w/v) polyethylene glycol 6000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.68→82.6 Å / Num. obs: 205822 / % possible obs: 94.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 4.9
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 0.553 / Num. unique obs: 10162

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TEP

6tep


Resolution: 1.68→82.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.609 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.308 10249 5 %RANDOM
Rwork0.2236 ---
obs0.2278 195339 94.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.67 Å2 / Biso mean: 24.385 Å2 / Biso min: 5.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0 Å2-1.88 Å2
2---1.07 Å20 Å2
3---2.86 Å2
Refinement stepCycle: final / Resolution: 1.68→82.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12381 0 520 764 13665
Biso mean--38.88 30.49 -
Num. residues----1668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01313499
X-RAY DIFFRACTIONr_bond_other_d0.0040.01712564
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.64318224
X-RAY DIFFRACTIONr_angle_other_deg1.4021.58329127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57751762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9122.422673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.146152068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9271592
X-RAY DIFFRACTIONr_chiral_restr0.0870.21748
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215371
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022743
X-RAY DIFFRACTIONr_rigid_bond_restr5.843326062
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 772 -
Rwork0.309 14590 -
all-15362 -
obs--96.11 %

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