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- PDB-8oqx: Crystal structure of Tannerella forsythia MurNAc kinase MurK with... -

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Basic information

Entry
Database: PDB / ID: 8oqx
TitleCrystal structure of Tannerella forsythia MurNAc kinase MurK with a phosphate analogue
ComponentsATPase
KeywordsTRANSFERASE / sugar phosphorylation
Function / homology: / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / DI(HYDROXYETHYL)ETHER / ATPase
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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

Downloads & links

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Assembly

Deposited unit
A: ATPase
B: ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,83116
Polymers62,6762
Non-polymers2,15514
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-109 kcal/mol
Surface area24350 Å2
Unit cell
Length a, b, c (Å)61.700, 55.650, 86.000
Angle α, β, γ (deg.)90.000, 93.596, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATPase


Mass: 31338.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: BFO_0042 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8UQH9

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Non-polymers , 7 types, 225 molecules

#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.12 - 0.14 M ammonium sulfate, Citric acid + Bis/Tris propane pH=5.5, PEG 3350 (14%-18% (w/v))

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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: Aug 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 33324 / % possible obs: 100 % / Redundancy: 6.84 % / CC1/2: 0.996 / Net I/σ(I): 10.37
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 2435 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→48.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.16 / SU B: 13.904 / SU ML: 0.174 / Average fsc free: 0.956 / Average fsc work: 0.9708 / Cross valid method: FREE R-VALUE / ESU R: 0.247 / ESU R Free: 0.196
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2351 1667 5.002 %
Rwork0.1886 31657 -
all0.191 --
obs-33324 99.979 %
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: 33.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0.295 Å2
2---0.978 Å2-0 Å2
3---0.828 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 127 211 4671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124598
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.6466240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.2691027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46910749
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.95810191
X-RAY DIFFRACTIONr_chiral_restr0.0920.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023363
X-RAY DIFFRACTIONr_nbd_refined0.2120.21891
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2226
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3340.210
X-RAY DIFFRACTIONr_mcbond_it1.3692.7742251
X-RAY DIFFRACTIONr_mcangle_it1.9783.5432811
X-RAY DIFFRACTIONr_scbond_it3.43.6372347
X-RAY DIFFRACTIONr_scangle_it4.3574.5223425
X-RAY DIFFRACTIONr_lrange_it9.35524.0436681
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
2.12-2.1750.3291220.30223080.30324320.9250.93799.91780.289
2.175-2.2340.3051200.2722800.27124010.9410.95199.95840.254
2.234-2.2990.3441160.24521970.2523130.9280.9611000.22
2.299-2.370.3041120.23521370.23822490.9410.9651000.206
2.37-2.4470.3191100.24120950.24522060.9330.96599.95470.207
2.447-2.5330.2681050.2519880.25120930.9550.9621000.213
2.533-2.6280.2321000.22219120.22320120.9640.971000.191
2.628-2.7350.241980.20718610.20919590.9610.9751000.173
2.735-2.8560.249960.20418190.20719150.960.9751000.172
2.856-2.9950.259900.18917070.19217970.960.9791000.157
2.995-3.1570.208860.17516280.17717140.9740.9811000.149
3.157-3.3470.215820.16415560.16716380.9760.9841000.145
3.347-3.5770.255760.17314450.17615210.9590.9841000.157
3.577-3.8620.202720.16513710.16714430.9740.9861000.152
3.862-4.2280.185660.14812610.1513270.980.9881000.137
4.228-4.7220.157600.13211400.13312000.9880.991000.125
4.722-5.4440.177530.14410020.14510550.980.9891000.135
5.444-6.6470.268450.1928620.1959070.9680.9811000.174
6.647-9.3140.242360.1716860.1757220.9690.9851000.165
9.314-48.610.23220.194020.1924240.9820.9821000.201
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)
14.1344-1.24411.55372.6930.03982.8183-0.0619-0.1593-0.01870.16370.0927-0.0435-0.1538-0.0503-0.03080.1550.0053-0.01540.26690.02810.0822-5.7926.760436.1427
22.2763-0.1373-2.27891.96181.76329.7563-0.0573-0.0917-0.09930.15340.08610.01890.09940.0023-0.02880.14160.009-0.05070.18750.03440.1694-5.1383-1.88932.2826
32.62911.1428-0.13593.3612-0.34161.60990.03290.2850.1943-0.10540.02040.29220.0037-0.0867-0.05330.03420.03320.00070.28470.01080.11339.159311.530514.9634
47.11620.8304-5.2520.3561-1.40987.818-0.05260.7243-0.2899-0.17630.06960.15090.1913-0.6315-0.0170.2682-0.0062-0.14730.2731-0.05470.2892-3.95720.66914.5081
54.61490.8163-0.23664.46420.11933.1179-0.0247-0.17170.02690.14910.0386-0.0361-0.120.0012-0.01390.17610-0.09230.2409-0.01250.097746.865528.663130.4237
61.9323-1.3063-0.37271.16441.82589.0471-0.140.14940.0716-0.026-0.0434-0.0037-0.54980.08890.18340.235-0.0956-0.06050.28920.03690.173143.954531.679316.0506
72.55121.2135-0.27642.848-0.98882.31370.03320.0812-0.12450.0178-0.072-0.1018-0.02230.13990.03880.02380.0102-0.02720.2749-0.01140.034831.456211.730815.5446
84.67593.53223.2594.95094.0546.1922-0.09190.6638-0.1167-0.36170.2935-0.5759-0.20210.6667-0.20160.14390.01950.04180.37910.03160.136845.582521.11649.353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 81
2X-RAY DIFFRACTION2ALLA82 - 105
3X-RAY DIFFRACTION3ALLA106 - 249
4X-RAY DIFFRACTION4ALLA250 - 278

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