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- PDB-8oqk: Crystal structure of Tannerella forsythia sugar kinase K1058 -

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Basic information

Entry
Database: PDB / ID: 8oqk
TitleCrystal structure of Tannerella forsythia sugar kinase K1058
ComponentsN-acetylglucosamine kinase
KeywordsTRANSFERASE / sugar phosphorylation
Function / homology: / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / BadF/BadG/BcrA/BcrD ATPase family protein
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGogler, K. / Fink, P. / Stasiak, A.C. / Stehle, T. / Zocher, G.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765042European Union
German Research Foundation (DFG) Germany
CitationJournal: J.Biol.Chem. / Year: 2023
Title: N-acetylmuramic acid recognition by MurK kinase from the MurNAc auxotrophic oral pathogen Tannerella forsythia.
Authors: Stasiak, A.C. / Gogler, K. / Borisova, M. / Fink, P. / Mayer, C. / Stehle, T. / Zocher, G.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0523
Polymers31,8981
Non-polymers1542
Water2,432135
1
A: N-acetylglucosamine kinase
hetero molecules

A: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1056
Polymers63,7972
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area3230 Å2
ΔGint-2 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.940, 131.940, 89.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-478-

HOH

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Components

#1: Protein N-acetylglucosamine kinase


Mass: 31898.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_0034 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UQH1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium cacodylate, MPD, PEG 8000 / PH range: 6.3 - 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.216 Å / Num. obs: 26844 / % possible obs: 100 % / Redundancy: 26.63 % / CC1/2: 0.999 / Net I/σ(I): 19.58
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1946 / CC1/2: 0.534

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X7F

1x7f


Resolution: 2→49.216 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.154 / SU B: 8.164 / SU ML: 0.107 / Average fsc free: 0.9644 / Average fsc work: 0.9737 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.126
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2057 1343 5.003 %
Rwork0.1771 25500 -
all0.179 --
obs-26843 99.985 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.513 Å2
Baniso -1Baniso -2Baniso -3
1--0.277 Å20 Å2-0 Å2
2---0.277 Å20 Å2
3---0.555 Å2
Refinement stepCycle: LAST / Resolution: 2→49.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 10 135 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122241
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.6313027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3355276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.6991014
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51210366
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.45710106
X-RAY DIFFRACTIONr_chiral_restr0.090.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021698
X-RAY DIFFRACTIONr_nbd_refined0.2070.2900
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2106
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.225
X-RAY DIFFRACTIONr_mcbond_it3.5945.7771107
X-RAY DIFFRACTIONr_mcangle_it4.0317.3481382
X-RAY DIFFRACTIONr_scbond_it5.7356.5381134
X-RAY DIFFRACTIONr_scangle_it6.8878.0461645
X-RAY DIFFRACTIONr_lrange_it8.26440.573307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.277980.31218450.3119430.9410.9371000.304
2.052-2.1080.258950.26318130.26319080.9480.9531000.244
2.108-2.1690.291920.21917510.22318430.9470.9681000.194
2.169-2.2360.224910.20617250.20718160.970.9721000.18
2.236-2.3090.234870.19316560.19617440.9640.97599.94270.163
2.309-2.390.254840.19416010.19716850.960.9751000.164
2.39-2.480.241820.19415600.19616420.9650.9761000.156
2.48-2.5810.258790.1915000.19415790.9580.9771000.158
2.581-2.6950.212760.1914340.19115100.9680.9781000.153
2.695-2.8260.223720.18113710.18314430.9680.9811000.151
2.826-2.9780.246690.17813160.18113850.9630.981000.146
2.978-3.1580.225660.18412420.18613080.9710.9791000.154
3.158-3.3750.174620.16711790.16712410.9820.9831000.148
3.375-3.6440.233580.16511020.16811600.9680.9841000.15
3.644-3.990.152540.15610260.15610800.9860.9871000.146
3.99-4.4570.13490.1349270.1349760.990.991000.126
4.457-5.140.138430.1398230.1398660.990.9891000.133
5.14-6.2780.257370.2047150.2077520.970.9781000.186
6.278-8.8070.226300.1765640.1785940.9760.9851000.173
8.807-49.2160.195190.1593500.1613690.9480.9811000.175
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)
13.64681.93753.03525.97614.74099.4699-0.07640.52260.0859-0.47130.08590.05940.02410.289-0.00950.21640.0889-0.0460.1893-0.02440.1698-6.0139-20.1246-27.5548
23.4627-1.95670.00335.9280.21481.40150.11450.09350.2183-0.3814-0.11340.5701-0.1811-0.4629-0.00110.16010.0672-0.08780.227-0.06340.2057-10.3679-16.9467-18.4911
31.84471.19730.11771.88110.05051.31040.00180.1807-0.0803-0.1920.0374-0.01520.0526-0.0233-0.03920.04670.0246-0.00180.0371-0.00330.008714.8084-20.588-11.2576
412.22950.15062.32581.16360.18675.66470.15180.864-0.244-0.497-0.29870.01910.2439-0.10290.14680.26750.1154-0.02420.1711-0.04780.0735-1.8889-28.5513-24.3393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 26
2X-RAY DIFFRACTION2ALLA27 - 106
3X-RAY DIFFRACTION3ALLA107 - 263
4X-RAY DIFFRACTION4ALLA264 - 278

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