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

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Basic information

Entry
Database: PDB / ID: 6tep
TitleCrystal structure of a galactokinase from Bifidobacterium infantis in complex with ADP
ComponentsGalactokinase
KeywordsTRANSFERASE / ADP / 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
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Galactokinase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.2Sep 30, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 1.3Jan 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
D: Galactokinase
C: Galactokinase
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,43538
Polymers183,2624
Non-polymers4,17434
Water26,5721475
1
A: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6288
Polymers45,8151
Non-polymers8137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7138
Polymers45,8151
Non-polymers8977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,98510
Polymers45,8151
Non-polymers1,1709
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,10912
Polymers45,8151
Non-polymers1,29411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.272, 164.495, 115.873
Angle α, β, γ (deg.)90.000, 95.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ADCB

#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 (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_2062 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7GUI0

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Non-polymers , 7 types, 1509 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1475 / 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: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→94.58 Å / Num. obs: 336915 / % possible obs: 98.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.3
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.663 / Num. unique obs: 16117 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PIE

1pie


Resolution: 1.45→94.58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.47 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.077
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Density insufficient to model residues 245-247 in chains A + B, 244-247 in chain C and 245 in chain D, as ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Density insufficient to model residues 245-247 in chains A + B, 244-247 in chain C and 245 in chain D, as well as the C-terminal His-tag in all chains.
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 16932 5 %RANDOM
Rwork0.184 ---
obs0.1871 319927 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 17.661 Å2 / Biso min: 5.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å2-0.95 Å2
2--0.43 Å20 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.45→94.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12295 0 261 1475 14031
Biso mean--25.45 30.14 -
Num. residues----1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01313198
X-RAY DIFFRACTIONr_bond_other_d0.0050.01712149
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.63817945
X-RAY DIFFRACTIONr_angle_other_deg1.6351.57828148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91851755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86522.365668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54152051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.291593
X-RAY DIFFRACTIONr_chiral_restr0.1070.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215319
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022733
X-RAY DIFFRACTIONr_rigid_bond_restr4.836325347
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 1238 -
Rwork0.31 22992 -
all-24230 -
obs--95.65 %

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