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- PDB-7b6n: Crystal structure of MurE from E.coli in complex with Z757284952 -

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Basic information

Entry
Database: PDB / ID: 7b6n
TitleCrystal structure of MurE from E.coli in complex with Z757284952
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 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, 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-SYZ / 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: 1.79 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 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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)107,3895
Polymers106,9872
Non-polymers4023
Water5,567309
1
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5562
Polymers53,4941
Non-polymers621
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)53,8343
Polymers53,4941
Non-polymers3402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
Unit cell
Length a, b, c (Å)58.046, 57.932, 74.110
Angle α, β, γ (deg.)96.99, 91.40, 105.44
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 (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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SYZ / N-(2-(2,4-dioxothiazolidin-3-yl)ethyl)-3-methylbenzamide / ~{N}-[2-[2,4-bis(oxidanylidene)-1,3-thiazolidin-3-yl]ethyl]-3-methyl-benzamide


Mass: 278.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 11.6% PEG4K 20.3% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.79→55.91 Å / Num. obs: 87528 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC1/2: 0.995 / Net I/σ(I): 4.8
Reflection shellResolution: 1.79→1.88 Å / Num. unique obs: 12354 / CC1/2: 0.419

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B53

7b53


Resolution: 1.79→55.91 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.302 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24283 4744 5.1 %RANDOM
Rwork0.21562 ---
obs0.21702 87528 95.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.534 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å21.69 Å20.27 Å2
2--0 Å20.61 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.79→55.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7282 0 27 309 7618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0187576
X-RAY DIFFRACTIONr_bond_other_d0.0010.027069
X-RAY DIFFRACTIONr_angle_refined_deg1.211.88210306
X-RAY DIFFRACTIONr_angle_other_deg1.0542.9316322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4965989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25723.874333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.996151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7881557
X-RAY DIFFRACTIONr_chiral_restr0.0710.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021526
X-RAY DIFFRACTIONr_mcbond_it2.183.7963928
X-RAY DIFFRACTIONr_mcbond_other2.183.7963929
X-RAY DIFFRACTIONr_mcangle_it3.3855.6794928
X-RAY DIFFRACTIONr_mcangle_other3.3845.6784928
X-RAY DIFFRACTIONr_scbond_it2.7024.2443648
X-RAY DIFFRACTIONr_scbond_other2.7024.2453649
X-RAY DIFFRACTIONr_scangle_other4.3016.2155377
X-RAY DIFFRACTIONr_long_range_B_refined6.2845.8958260
X-RAY DIFFRACTIONr_long_range_B_other6.26545.8148224

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