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- PDB-7b6j: Crystal structure of MurE from E.coli in complex with minifrag su... -

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Basic information

Entry
Database: PDB / ID: 7b6j
TitleCrystal structure of MurE from E.coli in complex with minifrag succinimide
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
ISOPROPYL ALCOHOL / succinimide / 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: 2.09 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 ...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 / refine_hist
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 / _refine_hist.d_res_low

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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)107,5239
Polymers106,9872
Non-polymers5367
Water5,765320
1
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8105
Polymers53,4941
Non-polymers3164
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)53,7134
Polymers53,4941
Non-polymers2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
Unit cell
Length a, b, c (Å)58.258, 58.291, 74.633
Angle α, β, γ (deg.)96.824, 91.360, 104.993
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-SZB / succinimide / pyrrolidine-2,5-dione / pyrrole-2,5-dione / 2,5-pyrrolidinedione


Mass: 97.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H3NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 11.6% PEG4K 18.4% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→47.61 Å / Num. obs: 68240 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4893 / CC1/2: 0.599 / % possible all: 96.7

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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: 2.09→47.61 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.087 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.174 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2361 3496 5.125 %
Rwork0.183 64712 -
all0.186 --
obs-68208 99.534 %
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: 41.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.159 Å22.354 Å20.502 Å2
2--0.721 Å20.994 Å2
3----2.208 Å2
Refinement stepCycle: LAST / Resolution: 2.09→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7282 0 37 320 7639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137575
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177204
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.63210302
X-RAY DIFFRACTIONr_angle_other_deg1.3311.58216529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68221.902389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.866151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5571556
X-RAY DIFFRACTIONr_chiral_restr0.0680.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021706
X-RAY DIFFRACTIONr_nbd_refined0.2050.21388
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.26498
X-RAY DIFFRACTIONr_nbtor_refined0.1520.23610
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23664
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1580.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.233
X-RAY DIFFRACTIONr_nbd_other0.2050.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3410.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.22
X-RAY DIFFRACTIONr_mcbond_it3.0594.1583929
X-RAY DIFFRACTIONr_mcbond_other3.0564.1573926
X-RAY DIFFRACTIONr_mcangle_it4.226.2164922
X-RAY DIFFRACTIONr_mcangle_other4.226.2164922
X-RAY DIFFRACTIONr_scbond_it3.9524.693646
X-RAY DIFFRACTIONr_scbond_other3.9514.693647
X-RAY DIFFRACTIONr_scangle_it5.9366.8495378
X-RAY DIFFRACTIONr_scangle_other5.9366.8495379
X-RAY DIFFRACTIONr_lrange_it7.22949.578089
X-RAY DIFFRACTIONr_lrange_other7.22949.5728090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3172620.3024589X-RAY DIFFRACTION95.7371
2.001-2.0560.312530.2714594X-RAY DIFFRACTION98.8377
2.056-2.1150.2862260.2474566X-RAY DIFFRACTION99.9374
2.115-2.180.2862400.2174477X-RAY DIFFRACTION99.873
2.18-2.2520.2332220.2074278X-RAY DIFFRACTION99.889
2.252-2.3310.2392370.1924156X-RAY DIFFRACTION99.9772
2.331-2.4190.271870.1884013X-RAY DIFFRACTION99.9762
2.419-2.5170.2432100.1933845X-RAY DIFFRACTION99.9507
2.517-2.6290.2432190.193679X-RAY DIFFRACTION100
2.629-2.7570.2552050.1783531X-RAY DIFFRACTION100
2.757-2.9060.2411820.1793351X-RAY DIFFRACTION99.9717
2.906-3.0820.2441640.1733179X-RAY DIFFRACTION100
3.082-3.2950.2291440.1742980X-RAY DIFFRACTION100
3.295-3.5580.2181530.1732791X-RAY DIFFRACTION100
3.558-3.8970.2591240.1742576X-RAY DIFFRACTION99.963
3.897-4.3550.1931260.152286X-RAY DIFFRACTION100
4.355-5.0260.2011140.1432047X-RAY DIFFRACTION100
5.026-6.1480.2461050.1931705X-RAY DIFFRACTION100
6.148-8.6650.168790.1531333X-RAY DIFFRACTION100
8.665-73.9850.251440.207736X-RAY DIFFRACTION99.6169

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