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- PDB-7b9w: Crystal structure of MurE from E.coli in complex with Z757284380 -

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Basic information

Entry
Database: PDB / ID: 7b9w
TitleCrystal structure of MurE from E.coli in complex with Z757284380
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-T4H / 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: 1.82 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 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 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)107,4105
Polymers106,9872
Non-polymers4233
Water5,459303
1
AAA: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6183
Polymers53,4941
Non-polymers1242
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)53,7922
Polymers53,4941
Non-polymers2991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.409, 58.621, 74.438
Angle α, β, γ (deg.)97.110, 91.540, 104.841
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-T4H / 3-Chloro-N-[2-(2,4-dioxo-1,3-thiazolidin-3-yl)ethyl]benzamide / ~{N}-[2-[2,4-bis(oxidanylidene)-1,3-thiazolidin-3-yl]ethyl]-3-chloranyl-benzamide


Mass: 298.745 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 11.9% PEG4K 20.1% 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: 1.78→56.36 Å / Num. obs: 88411 / % possible obs: 97.57 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.048 / Rrim(I) all: 0.088 / Net I/σ(I): 8.9
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.619 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 11841 / CC1/2: 0.314 / Rrim(I) all: 1.93 / % possible all: 96.3

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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: 1.82→56.34 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.005 / SU ML: 0.138 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2311 4460 5.112 %
Rwork0.1929 82786 -
all0.195 --
obs-87246 96.243 %
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: 39.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.332 Å20.914 Å2-0.362 Å2
2--0.592 Å20.244 Å2
3----0.825 Å2
Refinement stepCycle: LAST / Resolution: 1.82→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7282 0 27 303 7612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177202
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.63210306
X-RAY DIFFRACTIONr_angle_other_deg1.3171.58116528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5285989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32721.846390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.018151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0451557
X-RAY DIFFRACTIONr_chiral_restr0.0680.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021711
X-RAY DIFFRACTIONr_nbd_refined0.2050.21366
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.26448
X-RAY DIFFRACTIONr_nbtor_refined0.1520.23589
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23690
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.218
X-RAY DIFFRACTIONr_nbd_other0.2060.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.29
X-RAY DIFFRACTIONr_mcbond_it3.173.883928
X-RAY DIFFRACTIONr_mcbond_other3.163.8793927
X-RAY DIFFRACTIONr_mcangle_it4.5765.8014928
X-RAY DIFFRACTIONr_mcangle_other4.5755.8014929
X-RAY DIFFRACTIONr_scbond_it4.2774.5693648
X-RAY DIFFRACTIONr_scbond_other4.2764.5693649
X-RAY DIFFRACTIONr_scangle_it6.7026.6135376
X-RAY DIFFRACTIONr_scangle_other6.7016.6135377
X-RAY DIFFRACTIONr_lrange_it8.59646.5488010
X-RAY DIFFRACTIONr_lrange_other8.58746.4417970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.8260.42700.3925270X-RAY DIFFRACTION82.1593
1.826-1.8760.3742930.3695779X-RAY DIFFRACTION93.3867
1.876-1.9310.3543340.3265781X-RAY DIFFRACTION96.3144
1.931-1.990.2973090.2975625X-RAY DIFFRACTION96.645
1.99-2.0550.3083120.2695500X-RAY DIFFRACTION96.8667
2.055-2.1270.2962630.2455332X-RAY DIFFRACTION96.7324
2.127-2.2070.2612720.2185145X-RAY DIFFRACTION97.2706
2.207-2.2970.2482630.214961X-RAY DIFFRACTION97.4991
2.297-2.40.2472460.194850X-RAY DIFFRACTION97.7744
2.4-2.5160.2212480.1894540X-RAY DIFFRACTION97.8941
2.516-2.6520.2422600.1884373X-RAY DIFFRACTION98.0944
2.652-2.8130.2282300.1814084X-RAY DIFFRACTION98.2688
2.813-3.0070.2572110.1883874X-RAY DIFFRACTION98.4812
3.007-3.2480.2271830.1843677X-RAY DIFFRACTION98.6455
3.248-3.5570.2151710.1763334X-RAY DIFFRACTION98.7602
3.557-3.9750.2111540.1653015X-RAY DIFFRACTION98.6613
3.975-4.5880.1931430.1472678X-RAY DIFFRACTION99.1216
4.588-5.6140.1991320.1562252X-RAY DIFFRACTION99.3333
5.614-7.9160.2041020.1951747X-RAY DIFFRACTION99.5156
7.916-56.340.162640.161969X-RAY DIFFRACTION99.7104

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