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- PDB-8ow7: Crystal structure of Tannerella forsythia sugar kinase K1058 in c... -

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Basic information

Entry
Database: PDB / ID: 8ow7
TitleCrystal structure of Tannerella forsythia sugar kinase K1058 in complex with N-acetylmuramic acid (MurNAc)
ComponentsN-acetylglucosamine kinase
KeywordsTRANSFERASE / sugar phosphorylation
Function / homology: / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / N-acetyl-beta-muramic acid / BadF/BadG/BcrA/BcrD ATPase family protein
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsStasiak, A.C. / Gogler, K. / Fink, P. / 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 27, 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
Revision 1.2Nov 8, 2023Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosamine kinase
B: N-acetylglucosamine kinase
C: N-acetylglucosamine kinase
D: N-acetylglucosamine kinase
E: N-acetylglucosamine kinase
F: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,25225
Polymers198,2436
Non-polymers3,00819
Water00
1
A: N-acetylglucosamine kinase
C: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,24410
Polymers66,0812
Non-polymers1,1638
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-93 kcal/mol
Surface area22180 Å2
2
B: N-acetylglucosamine kinase
F: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1489
Polymers66,0812
Non-polymers1,0677
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-85 kcal/mol
Surface area22050 Å2
3
D: N-acetylglucosamine kinase
E: N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8606
Polymers66,0812
Non-polymers7794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-44 kcal/mol
Surface area22510 Å2
Unit cell
Length a, b, c (Å)143.750, 143.750, 210.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein
N-acetylglucosamine kinase


Mass: 33040.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_0034 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UQH1
#2: Sugar
ChemComp-AMU / N-acetyl-beta-muramic acid / N-acetyl-muramic acid / BETA-N-ACETYLMURAMIC ACID


Type: D-saccharide, beta linking / Mass: 293.270 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H19NO8 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2962.58
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop8.51.5 M ammonium sulfate, 0.1 M Tris pH 8.5, 12% (v/v) glycerol
2772vapor diffusion, sitting drop8.51.5 M ammonium sulfate, 0.1 M Tris pH 8.5, 12% (v/v) glycerol

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA11
SYNCHROTRONSLS X06DA21
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M-F1PIXELFeb 5, 2022
DECTRIS PILATUS 2M-F2PIXELFeb 5, 2022
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
Reflection

Entry-ID: 8OW7

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Diffraction-IDNet I/σ(I)
3.06-48.5854871210020.3874.280.9917.97
3.08-48.4664715399.87.540.97625.62
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
3.06-3.2377540.3631
3.08-3.2775000.9762

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→29.85 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.184 / SU B: 51.746 / SU ML: 0.39 / Average fsc free: 0.9449 / Average fsc work: 0.9556 / Cross valid method: FREE R-VALUE / ESU R Free: 0.405
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2454 1444 3.002 %
Rwork0.2192 46659 -
all0.22 --
obs-48103 99.855 %
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: 86.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å20.003 Å20 Å2
2--0.006 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.06→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13091 0 185 0 13276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01213563
X-RAY DIFFRACTIONr_angle_refined_deg0.6091.63218353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.60151656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.9551079
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.074102207
X-RAY DIFFRACTIONr_dihedral_angle_6_deg8.84810630
X-RAY DIFFRACTIONr_chiral_restr0.0460.22029
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210212
X-RAY DIFFRACTIONr_nbd_refined0.1610.25347
X-RAY DIFFRACTIONr_nbtor_refined0.3050.29233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.2285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0550.23
X-RAY DIFFRACTIONr_mcbond_it1.19710.5096642
X-RAY DIFFRACTIONr_mcangle_it2.0613.5118292
X-RAY DIFFRACTIONr_scbond_it1.26710.9476921
X-RAY DIFFRACTIONr_scangle_it2.07614.01210061
X-RAY DIFFRACTIONr_lrange_it5.52168.44119103
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
3.06-3.1390.4391050.36533900.36834950.8230.8931000.364
3.139-3.2240.3631010.33632680.33733700.9180.91799.97030.325
3.224-3.3160.322990.30932050.3133040.9290.9341000.292
3.316-3.4170.308970.29231100.29332070.9310.9391000.271
3.417-3.5270.304930.28330270.28431200.9380.9441000.259
3.527-3.6490.242910.26629350.26530260.9560.9531000.239
3.649-3.7850.244880.25428400.25329280.9570.9591000.227
3.785-3.9370.236840.22527050.22627890.9660.9671000.196
3.937-4.1090.251810.21226440.21327250.9620.9711000.186
4.109-4.3050.231780.19825190.19925970.9660.9751000.17
4.305-4.5330.208740.17623920.17624660.9710.9811000.153
4.533-4.8010.207710.17522870.17623580.9740.981000.151
4.801-5.1230.226660.17521460.17622120.9660.9811000.152
5.123-5.520.214630.1920190.1920820.9750.9761000.163
5.52-6.0260.253570.21318580.21519150.9630.971000.181
6.026-6.7030.291520.22816880.2317400.9450.9661000.197
6.703-7.6760.214480.19615300.19715780.970.9761000.175
7.676-9.250.166400.14613170.14613570.9850.9871000.138
9.25-12.4950.129330.13810620.13710950.9890.9881000.14
12.495-29.850.37220.2527170.2557390.9290.9591000.256
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)
12.2465-0.9628-0.30642.2852-0.72641.87190.0613-0.1219-0.2073-0.0374-0.1405-0.13910.06370.54620.07920.2102-0.10830.08920.32330.010.153385.5463-25.0425-10.5289
22.1186-0.1063-0.5442.8880.14052.02470.01230.23410.1899-0.088-0.0067-0.01860.00430.0039-0.00560.1961-0.12760.01190.23340.02010.018850.3266-45.62098.9662
33.33740.99690.04622.4861-0.26852.00520.18110.0096-0.0117-0.06770.04210.3128-0.0618-0.397-0.22320.2314-0.01560.04660.18050.02580.078952.2915-17.4212-7.7249
42.5381-1.16090.73991.7073-0.77243.7162-0.40060.05550.4983-0.20060.02520.0726-1.45760.19390.37531.1008-0.1929-0.32150.34310.01470.430267.8848-16.008141.8496
52.0618-0.47450.3263.33831.24382.6008-0.07920.11890.2996-0.35620.1002-0.3042-0.14661.2949-0.02110.2879-0.0880.10021.01260.11030.197887.2469-43.388534.1207
63.0275-0.0243-0.40421.01540.31362.5031-0.2504-0.003-0.553-0.12280.0776-0.29360.5940.90080.17280.51580.20010.17720.52680.07590.299277.2996-66.290712.9856
Refinement TLS groupSelection: ALL

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