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- PDB-8ow9: Crystal structure of Tannerella forsythia MurNAc kinase MurK in c... -

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Basic information

Entry
Database: PDB / ID: 8ow9
TitleCrystal structure of Tannerella forsythia MurNAc kinase MurK in complex with N-acetylmuramic acid (MurNAc)
ComponentsPutative novel MurNAc kinase
KeywordsTRANSFERASE / sugar phosphorylation
Function / homology
Function and homology information


Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #160 / : / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-acetyl-beta-muramic acid / Putative novel MurNAc kinase
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Putative novel MurNAc kinase
A: Putative novel MurNAc kinase
D: Putative novel MurNAc kinase
E: Putative novel MurNAc kinase
C: Putative novel MurNAc kinase
F: Putative novel MurNAc kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,05510
Polymers194,8826
Non-polymers1,1734
Water00
1
B: Putative novel MurNAc kinase
A: Putative novel MurNAc kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5474
Polymers64,9612
Non-polymers5872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-7 kcal/mol
Surface area23040 Å2
MethodPISA
2
D: Putative novel MurNAc kinase
E: Putative novel MurNAc kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5474
Polymers64,9612
Non-polymers5872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-7 kcal/mol
Surface area22790 Å2
MethodPISA
3
C: Putative novel MurNAc kinase
F: Putative novel MurNAc kinase


Theoretical massNumber of molelcules
Total (without water)64,9612
Polymers64,9612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-17 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.425, 113.425, 294.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Putative novel MurNAc kinase


Mass: 32480.295 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: murK, TFUB20_00044 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D3UBL2
#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.: 4 / 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
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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% PEG10000, 100 mM trisodium citrate pH 5.5, 2% v/v 1,4-dioxane

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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: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→49.13 Å / Num. obs: 49814 / % possible obs: 98.5 % / Redundancy: 14.1 % / CC1/2: 0.994 / Net I/σ(I): 8.06
Reflection shellResolution: 2.7→2.87 Å / Num. unique obs: 8018 / CC1/2: 0.466

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.13 Å / Cross valid method: FREE R-VALUE / σ(F): 569.45 / Phase error: 30.5926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2758 1504 3.02 %
Rwork0.2574 48294 -
obs0.2689 49798 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12772 0 80 0 12852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007913137
X-RAY DIFFRACTIONf_angle_d1.689717789
X-RAY DIFFRACTIONf_chiral_restr0.10242002
X-RAY DIFFRACTIONf_plane_restr0.00772305
X-RAY DIFFRACTIONf_dihedral_angle_d3.86259793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.790.32771340.31294319X-RAY DIFFRACTION94.82
2.79-2.890.32091380.30264442X-RAY DIFFRACTION96.99
2.89-3.010.3191370.30784449X-RAY DIFFRACTION96.95
3.01-3.140.29481380.29714457X-RAY DIFFRACTION96.93
3.14-3.310.30131370.28734433X-RAY DIFFRACTION96.94
3.31-3.520.33861370.31124440X-RAY DIFFRACTION96.4
3.52-3.790.3571260.31244048X-RAY DIFFRACTION88.25
3.79-4.170.30971320.27494295X-RAY DIFFRACTION93.51
4.17-4.770.24151390.22044465X-RAY DIFFRACTION96.9
4.77-6.010.26651370.25434457X-RAY DIFFRACTION96.87
6.01-45.080.25991400.23584496X-RAY DIFFRACTION96.85

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