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- PDB-7b53: Crystal structure of MurE from E.coli -

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Basic information

Entry
Database: PDB / ID: 7b53
TitleCrystal structure of MurE from E.coli
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 cycle / 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 family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Jan 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
Item: _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
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)107,2356
Polymers106,9872
Non-polymers2484
Water7,620423
1
A: 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
B: 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
Unit cell
Length a, b, c (Å)58.631, 58.944, 74.228
Angle α, β, γ (deg.)97.32, 91.54, 105.17
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 K12 (bacteria) / 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) / Variant (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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 14% PEG4K 20% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→56.4 Å / Num. obs: 92515 / % possible obs: 96.6 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 1.3 % / Num. unique obs: 6655 / CC1/2: 0.495 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1e8c

1e8c


Resolution: 1.75→56.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.301 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21971 4440 4.8 %RANDOM
Rwork0.19525 ---
obs0.19645 88075 96.49 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.196 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20.96 Å2-0.17 Å2
2--0.93 Å20.6 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→56.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7284 0 16 424 7724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0187564
X-RAY DIFFRACTIONr_bond_other_d0.0010.027065
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.8810287
X-RAY DIFFRACTIONr_angle_other_deg1.0432.92816313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74323.874333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.508151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0321557
X-RAY DIFFRACTIONr_chiral_restr0.0670.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021521
X-RAY DIFFRACTIONr_mcbond_it2.1191.9613928
X-RAY DIFFRACTIONr_mcbond_other2.1171.9613927
X-RAY DIFFRACTIONr_mcangle_it2.9352.9284927
X-RAY DIFFRACTIONr_mcangle_other2.9362.9294928
X-RAY DIFFRACTIONr_scbond_it3.0992.3513636
X-RAY DIFFRACTIONr_scbond_other3.0992.3523637
X-RAY DIFFRACTIONr_scangle_other4.5423.3865359
X-RAY DIFFRACTIONr_long_range_B_refined6.54624.6688291
X-RAY DIFFRACTIONr_long_range_B_other6.51624.3788225
LS refinement shellResolution: 1.75→1.795 Å
RfactorNum. reflection% reflection
Rfree0.323 313 -
Rwork0.335 6259 -
obs--92.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.06790.4093-0.2044.2483-0.63255.2027-0.1480.23850.2472-0.17530.0532-0.0155-0.1704-0.04280.09480.14990.01010.05630.1490.0130.0479-24.32818.673-41.69
23.6289-1.0147-1.89250.56790.481.5058-0.03990.29170.1597-0.11090.0349-0.0424-0.0763-0.03150.0050.1896-0.0175-0.00350.15260.05090.0345-38.88323.394-29.763
39.1942-5.01376.05182.7868-2.99845.77970.08870.09240.0446-0.0414-0.09-0.0264-0.019-0.22410.00130.20420.04410.03590.1188-0.00110.0866-59.4310.444-36.016
45.9863-0.0969-2.26261.8710.553.1416-0.09870.3248-0.2862-0.06520.04960.26110.1465-0.2970.04910.13550.0279-0.0050.07720.01910.0642-58.52914.848-19.602
53.3553-2.12271.44933.1236-0.99692.7136-0.2392-0.26360.08480.29270.24650.1894-0.1648-0.1194-0.00730.14570.06740.01520.04210.00690.0379-59.22932.052-13.536
61.7679-0.52140.47432.2649-1.82924.83070.14840.0239-0.2101-0.28340.12080.17780.33350.0133-0.26920.13440.0352-0.03110.03370.00340.0397-68.98645.113-37.29
71.331-0.32090.13814.348-0.94695.67090.07390.01590.1409-0.03110.0092-0.2706-0.30430.4355-0.08310.12660.01670.00510.0655-0.00640.0394-63.59953.989-33.204
85.4090.77370.62475.6578-0.2624.59650.1752-0.84910.61060.6388-0.37390.284-0.5854-0.1760.19870.40340.02780.05110.3997-0.24140.176-45.26332.20215.369
92.4259-1.0855-0.89512.57360.80091.89410.0396-0.32280.27510.2467-0.0187-0.2175-0.11650.0985-0.02090.12970.0153-0.02050.1158-0.01350.0494-30.46917.8420.048
1012.152-1.8672-4.97150.77521.21536.36790.0754-0.2962-0.65670.0209-0.0554-0.29450.33470.306-0.020.1443-0.0062-0.01010.2370.05410.3705-42.0730.3316.651
111.9099-0.574-0.35514.06990.98492.2519-0.0339-0.0865-0.41880.1946-0.08090.29910.1857-0.13730.11490.11290.0208-0.00320.09330.02680.1088-36.999-1.917-7.552
124.7513-1.48071.65632.4897-1.23262.37760.09630.3577-0.1619-0.096-0.1069-0.07520.08790.19990.01060.07580.05380.01870.08150.0060.0197-20.4192.749-12.676
131.2752-0.06681.12341.50690.19264.86540.1712-0.1044-0.08530.0874-0.01770.06860.2392-0.1185-0.15350.07580.02740.00820.06870.02790.0184-5.749-3.64610.671
142.55570.54740.29142.7412-0.09424.67950.03320.02890.27090.121-0.0457-0.2104-0.23940.30080.01250.06310.02650.00670.09220.02370.0611.263.377.311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 68
2X-RAY DIFFRACTION2A69 - 208
3X-RAY DIFFRACTION3A209 - 227
4X-RAY DIFFRACTION4A228 - 274
5X-RAY DIFFRACTION5A275 - 340
6X-RAY DIFFRACTION6A341 - 436
7X-RAY DIFFRACTION7A437 - 495
8X-RAY DIFFRACTION8B4 - 92
9X-RAY DIFFRACTION9B93 - 205
10X-RAY DIFFRACTION10B206 - 229
11X-RAY DIFFRACTION11B230 - 274
12X-RAY DIFFRACTION12B275 - 342
13X-RAY DIFFRACTION13B343 - 433
14X-RAY DIFFRACTION14B434 - 495

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