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

ID or keywords:

Entry

Database: PDB / ID: 7b53

Title

Crystal structure of MurE from E.coli

Components

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase

Keywords

BIOSYNTHETIC 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

Biological species

Escherichia coli K12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Koekemoer, 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)

Citation

Journal: 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

Deposition	Dec 3, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2020	Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2	Jan 31, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7b53.cif.gz	385.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7b53_validation.pdf.gz	450.9 KB	Display	wwPDB validaton report
Full document	7b53_full_validation.pdf.gz	454.5 KB	Display
Data in XML	7b53_validation.xml.gz	37.3 KB	Display
Data in CIF	7b53_validation.cif.gz	54.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b5/7b53 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b53	HTTPS FTP

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Related structure data

Related structure data	7b60C 7b61C 7b68C 7b6gC 7b6iC 7b6jC 7b6kC 7b6lC 7b6mC 7b6nC 7b6oC 7b6pC 7b6qC 7b9eC 7b9wC 1e8cS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7b6l-1 7b6o-1 7b6m-1 7b60-1 7b6g-1 7b6n-1 7b9w-1 7b61-1 7b9e-2 7b6k-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

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

107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase

hetero molecules

defined by author
Evidence: gel filtration
53.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase

hetero molecules

defined by author
53.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	1
Space group name H-M	P1

#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 Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.31 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.75→56.4 Å / Num. obs: 92515 / % possible obs: 96.6 % / Redundancy: 1.9 % / CC_1/2: 0.997 / Net I/σ(I): 8.4
Reflection shell	Resolution: 1.75→1.8 Å / Redundancy: 1.3 % / Num. unique obs: 6655 / CC_1/2: 0.495 / % possible all: 93.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1e8c

1e8c

Resolution: 1.75→56.34 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21971	4440	4.8 %	RANDOM
R_work	0.19525	-	-	-
obs	0.19645	88075	96.49 %	-

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 38.196 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.98 Å²	0.96 Å²	-0.17 Å²
2-	-	0.93 Å²	0.6 Å²
3-	-	-	-0.75 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→56.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7284	0	16	424	7724

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.018	7564
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7065
X-RAY DIFFRACTION	r_angle_refined_deg	1.157	1.88	10287
X-RAY DIFFRACTION	r_angle_other_deg	1.043	2.928	16313
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.351	5	989
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.743	23.874	333
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.508	15	1224
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.032	15	57
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1171
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	8656
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1521
X-RAY DIFFRACTION	r_mcbond_it	2.119	1.961	3928
X-RAY DIFFRACTION	r_mcbond_other	2.117	1.961	3927
X-RAY DIFFRACTION	r_mcangle_it	2.935	2.928	4927
X-RAY DIFFRACTION	r_mcangle_other	2.936	2.929	4928
X-RAY DIFFRACTION	r_scbond_it	3.099	2.351	3636
X-RAY DIFFRACTION	r_scbond_other	3.099	2.352	3637
X-RAY DIFFRACTION	r_scangle_other	4.542	3.386	5359
X-RAY DIFFRACTION	r_long_range_B_refined	6.546	24.668	8291
X-RAY DIFFRACTION	r_long_range_B_other	6.516	24.378	8225

LS refinement shell

Resolution: 1.75→1.795 Å

	R_factor	Num. reflection	% reflection
R_free	0.323	313	-
R_work	0.335	6259	-
obs	-	-	92.39 %

Refinement TLS params.

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

ID	L11 (°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)
1	5.0679	0.4093	-0.204	4.2483	-0.6325	5.2027	-0.148	0.2385	0.2472	-0.1753	0.0532	-0.0155	-0.1704	-0.0428	0.0948	0.1499	0.0101	0.0563	0.149	0.013	0.0479	-24.328	18.673	-41.69
2	3.6289	-1.0147	-1.8925	0.5679	0.48	1.5058	-0.0399	0.2917	0.1597	-0.1109	0.0349	-0.0424	-0.0763	-0.0315	0.005	0.1896	-0.0175	-0.0035	0.1526	0.0509	0.0345	-38.883	23.394	-29.763
3	9.1942	-5.0137	6.0518	2.7868	-2.9984	5.7797	0.0887	0.0924	0.0446	-0.0414	-0.09	-0.0264	-0.019	-0.2241	0.0013	0.2042	0.0441	0.0359	0.1188	-0.0011	0.0866	-59.43	10.444	-36.016
4	5.9863	-0.0969	-2.2626	1.871	0.55	3.1416	-0.0987	0.3248	-0.2862	-0.0652	0.0496	0.2611	0.1465	-0.297	0.0491	0.1355	0.0279	-0.005	0.0772	0.0191	0.0642	-58.529	14.848	-19.602
5	3.3553	-2.1227	1.4493	3.1236	-0.9969	2.7136	-0.2392	-0.2636	0.0848	0.2927	0.2465	0.1894	-0.1648	-0.1194	-0.0073	0.1457	0.0674	0.0152	0.0421	0.0069	0.0379	-59.229	32.052	-13.536
6	1.7679	-0.5214	0.4743	2.2649	-1.8292	4.8307	0.1484	0.0239	-0.2101	-0.2834	0.1208	0.1778	0.3335	0.0133	-0.2692	0.1344	0.0352	-0.0311	0.0337	0.0034	0.0397	-68.986	45.113	-37.29
7	1.331	-0.3209	0.1381	4.348	-0.9469	5.6709	0.0739	0.0159	0.1409	-0.0311	0.0092	-0.2706	-0.3043	0.4355	-0.0831	0.1266	0.0167	0.0051	0.0655	-0.0064	0.0394	-63.599	53.989	-33.204
8	5.409	0.7737	0.6247	5.6578	-0.262	4.5965	0.1752	-0.8491	0.6106	0.6388	-0.3739	0.284	-0.5854	-0.176	0.1987	0.4034	0.0278	0.0511	0.3997	-0.2414	0.176	-45.263	32.202	15.369
9	2.4259	-1.0855	-0.8951	2.5736	0.8009	1.8941	0.0396	-0.3228	0.2751	0.2467	-0.0187	-0.2175	-0.1165	0.0985	-0.0209	0.1297	0.0153	-0.0205	0.1158	-0.0135	0.0494	-30.469	17.842	0.048
10	12.152	-1.8672	-4.9715	0.7752	1.2153	6.3679	0.0754	-0.2962	-0.6567	0.0209	-0.0554	-0.2945	0.3347	0.306	-0.02	0.1443	-0.0062	-0.0101	0.237	0.0541	0.3705	-42.073	0.331	6.651
11	1.9099	-0.574	-0.3551	4.0699	0.9849	2.2519	-0.0339	-0.0865	-0.4188	0.1946	-0.0809	0.2991	0.1857	-0.1373	0.1149	0.1129	0.0208	-0.0032	0.0933	0.0268	0.1088	-36.999	-1.917	-7.552
12	4.7513	-1.4807	1.6563	2.4897	-1.2326	2.3776	0.0963	0.3577	-0.1619	-0.096	-0.1069	-0.0752	0.0879	0.1999	0.0106	0.0758	0.0538	0.0187	0.0815	0.006	0.0197	-20.419	2.749	-12.676
13	1.2752	-0.0668	1.1234	1.5069	0.1926	4.8654	0.1712	-0.1044	-0.0853	0.0874	-0.0177	0.0686	0.2392	-0.1185	-0.1535	0.0758	0.0274	0.0082	0.0687	0.0279	0.0184	-5.749	-3.646	10.671
14	2.5557	0.5474	0.2914	2.7412	-0.0942	4.6795	0.0332	0.0289	0.2709	0.121	-0.0457	-0.2104	-0.2394	0.3008	0.0125	0.0631	0.0265	0.0067	0.0922	0.0237	0.061	1.26	3.37	7.311

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 68
2	X-RAY DIFFRACTION	2	A	69 - 208
3	X-RAY DIFFRACTION	3	A	209 - 227
4	X-RAY DIFFRACTION	4	A	228 - 274
5	X-RAY DIFFRACTION	5	A	275 - 340
6	X-RAY DIFFRACTION	6	A	341 - 436
7	X-RAY DIFFRACTION	7	A	437 - 495
8	X-RAY DIFFRACTION	8	B	4 - 92
9	X-RAY DIFFRACTION	9	B	93 - 205
10	X-RAY DIFFRACTION	10	B	206 - 229
11	X-RAY DIFFRACTION	11	B	230 - 274
12	X-RAY DIFFRACTION	12	B	275 - 342
13	X-RAY DIFFRACTION	13	B	343 - 433
14	X-RAY DIFFRACTION	14	B	434 - 495

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