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- PDB-7b6g: Crystal structure of MurE from E.coli in complex with Z1675346324 -

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Basic information

Entry
Database: PDB / ID: 7b6g
TitleCrystal structure of MurE from E.coli in complex with Z1675346324
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 / cell cycle / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / ATP binding / cytoplasm
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, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
Chem-NUJ / 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: 1.937 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 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,3515
Polymers106,9872
Non-polymers3643
Water4,792266
1
AAA: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5722
Polymers53,4941
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7793
Polymers53,4941
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.276, 58.293, 74.115
Angle α, β, γ (deg.)97.234, 91.447, 105.313
Int Tables number1
Space group name H-MP1

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Components

#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 (E. coli) / Gene: murE, GHR40_01000, NCTC12650_04426 / Plasmid: pNIC28-Bsa4
Details (production host): N-terminal His6-tag -Twin-Strep-tag II -TEV-cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-Rosetta
References: UniProt: A0A5Q2GBT0, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-NUJ / trans-3-[(2,6-dimethylpyrimidin-4-yl)(methyl)amino]cyclobutan-1-ol


Mass: 207.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 23% PEG4K 16% 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: 1.94→73.42 Å / Num. obs: 66302 / % possible obs: 96 % / Redundancy: 1.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 1.7 % / Num. unique obs: 8015 / CC1/2: 0.672

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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: 1.937→73.388 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.019 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.178
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2557 3393 5.12 %
Rwork0.2049 62881 -
all0.207 --
obs-66274 95.596 %
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: 39.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.064 Å21.729 Å20.361 Å2
2--0.137 Å21.354 Å2
3----1.594 Å2
Refinement stepCycle: LAST / Resolution: 1.937→73.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7251 0 23 266 7540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137528
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177182
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.63110240
X-RAY DIFFRACTIONr_angle_other_deg1.2751.58216472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11721.783387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.569151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9221557
X-RAY DIFFRACTIONr_chiral_restr0.0650.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021696
X-RAY DIFFRACTIONr_nbd_refined0.2070.21346
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.26616
X-RAY DIFFRACTIONr_nbtor_refined0.1510.23541
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.226
X-RAY DIFFRACTIONr_nbd_other0.2030.2100
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2790.210
X-RAY DIFFRACTIONr_mcbond_it2.9393.9583902
X-RAY DIFFRACTIONr_mcbond_other2.9383.9593903
X-RAY DIFFRACTIONr_mcangle_it4.1225.9174888
X-RAY DIFFRACTIONr_mcangle_other4.1225.9174889
X-RAY DIFFRACTIONr_scbond_it3.5374.4623626
X-RAY DIFFRACTIONr_scbond_other3.5374.4623627
X-RAY DIFFRACTIONr_scangle_it5.3736.5225348
X-RAY DIFFRACTIONr_scangle_other5.3736.5235349
X-RAY DIFFRACTIONr_lrange_it6.99446.7487903
X-RAY DIFFRACTIONr_lrange_other6.9846.6967874
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
1.937-1.9870.3192300.3143520.3150940.7140.71589.9490.306
1.987-2.0420.3462580.29644600.29950200.6870.71993.98410.289
2.042-2.1010.3162140.27643740.27848490.7890.80994.61740.269
2.101-2.1650.2982250.26442910.26647550.7990.81894.97370.248
2.165-2.2360.3042220.27641230.27745550.6650.72295.38970.257
2.236-2.3150.2762400.23139960.23344440.8650.87595.31950.214
2.315-2.4020.3191760.21439080.21942370.8570.89596.3890.193
2.402-2.50.2772100.22237220.22541020.8630.89195.85570.2
2.5-2.6110.2861990.20935870.21339450.8920.91595.96960.187
2.611-2.7380.2972070.21634750.2237950.8790.90997.02240.197
2.738-2.8860.2371730.20532690.20735440.9210.92497.12190.187
2.886-3.0610.2861660.21231540.21534120.8870.91197.30360.194
3.061-3.2720.2521480.19529180.19731660.9070.93296.84140.184
3.272-3.5330.2561480.19427170.19729630.9140.93796.69250.187
3.533-3.870.2461160.18625430.18927460.9070.93596.83180.184
3.87-4.3250.211280.16222580.16424440.9560.96397.62680.164
4.325-4.9910.1931110.15120080.15321860.9540.96896.9350.156
4.991-6.1060.2731000.19616470.218170.9280.94596.14750.196
6.106-8.6050.2780.18113390.18214400.9520.95498.40280.187
8.605-73.3880.185440.1847400.1847900.9670.96899.24050.191

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