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- PDB-7b6p: Crystal structure of E.coli MurE - C269S C340S C450S in complex w... -

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Basic information

Entry
Database: PDB / ID: 7b6p
TitleCrystal structure of E.coli MurE - C269S C340S C450S in complex with Ellman's reagent
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
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 division / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily ...UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, 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 / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-phenyl-2-selanylbenzamide / CITRIC ACID / ISOPROPYL ALCOHOL / 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: 1.68 Å
AuthorsKoekemoer, L. / Steindel, M. / Fairhead, M. / 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. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T.
History
DepositionDec 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)108,07010
Polymers106,8912
Non-polymers1,1798
Water6,071337
1
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0345
Polymers53,4451
Non-polymers5894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
2
B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0365
Polymers53,4451
Non-polymers5904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
Unit cell
Length a, b, c (Å)58.590, 58.940, 74.380
Angle α, β, γ (deg.)96.720, 91.480, 104.470
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: 53445.320 Da / Num. of mol.: 2 / Mutation: C269S C340S C450S
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, 345 molecules

#2: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 13% PEG4K 19.5% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.68→56.6 Å / Num. obs: 105615 / % possible obs: 97 % / Redundancy: 3.6 % / CC1/2: 0.999 / Net I/σ(I): 12.1
Reflection shellResolution: 1.68→1.72 Å / Num. unique obs: 7696 / CC1/2: 0.384

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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: 1.68→56.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.486 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2392 5286 5.005 %
Rwork0.197 100321 -
all0.199 --
obs-105607 96.981 %
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: 37.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.626 Å20.715 Å20.036 Å2
2--0.226 Å21.149 Å2
3----0.341 Å2
Refinement stepCycle: LAST / Resolution: 1.68→56.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7217 0 74 337 7628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177140
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6310193
X-RAY DIFFRACTIONr_angle_other_deg1.3751.57916368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52721.921380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.886151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5211555
X-RAY DIFFRACTIONr_chiral_restr0.0710.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028676
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021686
X-RAY DIFFRACTIONr_nbd_refined0.2080.21346
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.26456
X-RAY DIFFRACTIONr_nbtor_refined0.1560.23624
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1410.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.213
X-RAY DIFFRACTIONr_nbd_other0.1530.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_mcbond_it2.9313.6663869
X-RAY DIFFRACTIONr_mcbond_other2.9283.6653868
X-RAY DIFFRACTIONr_mcangle_it4.0125.4854841
X-RAY DIFFRACTIONr_mcangle_other4.0135.4854842
X-RAY DIFFRACTIONr_scbond_it3.9884.2263630
X-RAY DIFFRACTIONr_scbond_other3.9884.2273631
X-RAY DIFFRACTIONr_scangle_it6.0116.1455350
X-RAY DIFFRACTIONr_scangle_other6.016.1465351
X-RAY DIFFRACTIONr_lrange_it7.24443.7897960
X-RAY DIFFRACTIONr_lrange_other7.22843.77918
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
1.68-1.7240.3724140.37472730.37480780.4790.4995.15970.376
1.724-1.7710.3664090.32670550.32978000.6060.61695.69230.318
1.771-1.8220.3273770.3169800.31176490.7030.71696.18250.296
1.822-1.8780.3313370.28267730.28473780.7740.78996.36760.265
1.878-1.940.3193200.27565640.27772040.7910.81795.5580.253
1.94-2.0080.2883000.23263900.23469310.8660.88296.52290.208
2.008-2.0830.2913070.23961840.24267280.8650.8896.47740.216
2.083-2.1680.272870.2160030.21264730.8990.91597.17290.191
2.168-2.2650.2553090.256900.20262110.9110.93596.58670.182
2.265-2.3750.2353250.19154250.19458860.9240.93597.68940.176
2.375-2.5030.252870.18851760.19155900.9270.94297.72810.176
2.503-2.6550.2372650.18750030.18953770.9340.94697.97280.177
2.655-2.8370.222700.18845900.1949710.9340.94397.76710.182
2.837-3.0640.2282130.20443520.20546520.9310.9498.12980.203
3.064-3.3560.2292050.19840220.19942890.9380.94598.55440.202
3.356-3.750.2381770.19436310.19638690.9320.94998.42340.201
3.75-4.3270.211500.16532230.16734140.9540.95998.79910.186
4.327-5.2920.1941480.15527430.15729220.9610.96998.93910.18
5.292-7.4510.2711140.18820980.19222290.9420.96299.23730.216
7.451-56.6040.173720.15711460.15812410.9690.9798.14670.189

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