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- PDB-7b6k: Crystal structure of MurE from E.coli in complex with Z57715447 -

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Basic information

Entry
Database: PDB / ID: 7b6k
TitleCrystal structure of MurE from E.coli in complex with Z57715447
ComponentsUDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
KeywordsBIOSYNTHETIC PROTEIN / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2 / 6-diaminopimelate ligase cell wall biosynthesis ligase drug target / Structural Genomics / Structural Genomics Consortium / SGC / fragment screening
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
CITRIC ACID / ISOPROPYL ALCOHOL / 5-cyclohexyl-3-(pyridin-4-yl)-1,2,4-oxadiazole / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.838 Å
AuthorsKoekemoer, L. / Steindel, M. / Fairhead, M. / Talon, R. / Douangamath, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of MurE from E.coli
Authors: Koekemoer, L. / Steindel, M. / Fairhead, M. / Talon, R. / Douangamath, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T.
History
DepositionDec 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0469
Polymers106,9872
Non-polymers1,0597
Water5,765320
1
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0535
Polymers53,4941
Non-polymers5604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9934
Polymers53,4941
Non-polymers5003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.693, 58.903, 74.011
Angle α, β, γ (deg.)97.098, 91.201, 104.598
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso- ...Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase / UDP-MurNAc-tripeptide synthetase / UDP-N-acetylmuramyl-tripeptide synthetase


Mass: 53493.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: murE, b0085, JW0083 / Plasmid: pNIC28-Bsa4
Details (production host): N-terminal His6-tag -Twin-Strep-tag II -TEV-cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): -R3-Rosetta
References: UniProt: P22188, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase

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Non-polymers , 5 types, 327 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-SZ2 / 5-cyclohexyl-3-(pyridin-4-yl)-1,2,4-oxadiazole / 5-cyclohexyl-3-pyridin-4-yl-1,2,4-oxadiazole


Mass: 229.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 21% PEG4K 22% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.77→73.27 Å / Num. obs: 87747 / % possible obs: 95.1 % / Redundancy: 1.8 % / CC1/2: 0.999 / Net I/σ(I): 8.2
Reflection shellResolution: 1.77→1.87 Å / Num. unique obs: 12825 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B53

7b53


Resolution: 1.838→73.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.65 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2559 4051 5.124 %
Rwork0.2057 75001 -
all0.208 --
obs-79052 95.562 %
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: 38.445 Å2
Baniso -1Baniso -2Baniso -3
1--0.035 Å21.49 Å2-0.701 Å2
2--0.917 Å20.832 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.838→73.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 72 320 7607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137538
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177176
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.63410253
X-RAY DIFFRACTIONr_angle_other_deg1.3281.58516469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85921.942381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.499151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9531555
X-RAY DIFFRACTIONr_chiral_restr0.0670.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021686
X-RAY DIFFRACTIONr_nbd_refined0.2040.21421
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.26664
X-RAY DIFFRACTIONr_nbtor_refined0.1540.23600
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2321
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3040.220
X-RAY DIFFRACTIONr_nbd_other0.2330.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2590.213
X-RAY DIFFRACTIONr_mcbond_it3.0933.8263894
X-RAY DIFFRACTIONr_mcbond_other3.0933.8263895
X-RAY DIFFRACTIONr_mcangle_it4.2685.7244883
X-RAY DIFFRACTIONr_mcangle_other4.2675.7234882
X-RAY DIFFRACTIONr_scbond_it3.7964.3583644
X-RAY DIFFRACTIONr_scbond_other3.7854.3583641
X-RAY DIFFRACTIONr_scangle_it5.6776.3575368
X-RAY DIFFRACTIONr_scangle_other5.6766.3585369
X-RAY DIFFRACTIONr_lrange_it7.18645.8088052
X-RAY DIFFRACTIONr_lrange_other7.17445.7258009
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
1.838-1.8860.3482770.31353860.31561250.6410.64492.45710.312
1.886-1.9380.3483000.33253100.33359290.6510.66794.61970.333
1.938-1.9940.2872900.26451780.26557960.8040.81594.34090.255
1.994-2.0550.3172840.26650090.26856570.8050.82393.56550.252
2.055-2.1220.2932410.23749530.23954590.8560.88195.14560.22
2.122-2.1970.2922470.23647550.23852440.8570.87795.38520.216
2.197-2.280.2852530.23845990.2451150.8840.994.85830.22
2.28-2.3730.2862380.20744770.21148970.8890.91896.28340.187
2.373-2.4780.2632130.19542990.19847050.9060.93295.8980.18
2.478-2.5990.2792350.21340650.21744830.8940.91395.91790.197
2.599-2.7390.2812280.20439250.20942880.8960.9296.85170.192
2.739-2.9050.2392030.19837140.240330.9360.93697.12370.188
2.905-3.1050.31860.21935570.22238380.8880.91797.52470.209
3.105-3.3540.2521550.20432370.20735010.9190.92996.88660.201
3.354-3.6730.2531750.20329910.20632760.9130.93796.64220.203
3.673-4.1050.2311390.18527070.18729190.9410.94997.49910.188
4.105-4.7380.2011220.15324060.15526050.9530.96597.04410.163
4.738-5.7970.2081170.1819910.18221940.9530.95996.08020.19
5.797-8.1720.225940.1915700.19317010.9450.94797.82480.2
8.172-73.3350.222540.1788710.189370.9580.9698.71930.188

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