PDB-2xja: Structure of MurE from M.tuberculosis with dipeptide and ADP

ID or keywords:

Entry

Database: PDB / ID: 2xja

Title

Structure of MurE from M.tuberculosis with dipeptide and ADP

Components

UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE

Keywords

LIGASE / PEPTIDOGLYCAN / PEPTIDASE LIGASE

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 / cell cycle / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / ATP binding / plasma membrane ...
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Basavannacharya, C. / Moody, P.R. / Bhakta, S. / Keep, N.

Citation

Journal: Protein Cell / Year: 2010
Title: Essential Residues for the Enzyme Activity of ATP-Dependent Mure Ligase from Mycobacterium Tuberculosis.
Authors: Basavannacharya, C. / Moody, P.R. / Munshi, T. / Cronin, N. / Keep, N.H. / Bhakta, S.

History

Deposition	Jul 3, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 18, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xja.cif.gz	746.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2xja.ent.gz	615.7 KB	Display	PDB format
PDBx/mmJSON format	2xja.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2xja_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	2xja_full_validation.pdf.gz	2.6 MB	Display
Data in XML	2xja_validation.xml.gz	79.4 KB	Display
Data in CIF	2xja_validation.cif.gz	102.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xj/2xja ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xja	HTTPS FTP

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Related structure data

Related structure data	2wtzS S: Starting model for refinement
Similar structure data	1jdy-1 6bmw-1 2wtz-4 2wtz-1 6mdd-2 4ohd-d 4ohl-2 5ibm-1 1uiu-1 2wtz-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) 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

Related structure data

2wtzS

S: Starting model for refinement

Similar structure data

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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

C: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE

D: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE

hetero molecules

227 kDa, 4 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&software
56.8 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&software
56.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE

hetero molecules

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

4

D: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.040, 76.320, 81.990
Angle α, β, γ (deg.)	111.32, 91.42, 92.90
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
3	1	D
4	1	C
1	2	B
2	2	A
1	3	B
2	3	A
3	3	C
4	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	B	25 - 378
2	1	1	2	A	25 - 378
3	1	1	2	D	25 - 378
4	1	1	2	C	25 - 378
1	1	2	1	B	379 - 535
2	1	2	1	A	379 - 535
1	1	3	4	B	1400 - 1500
2	1	3	4	A	1400 - 1500
3	1	3	4	C	1400 - 1500
4	1	3	4	D	1400 - 1500

NCS ensembles :

ID
1
2
3

#1: Protein	UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE / MURE / UDP-MURNAC-L-ALA-D-GLU\:MESO-DIAMINOPIMELATE LIGASE / MESO-DIAMINOPIMELATE-ADDING ENZYME / ...MURE / UDP-MURNAC-L-ALA-D-GLU\:MESO-DIAMINOPIMELATE LIGASE / MESO-DIAMINOPIMELATE-ADDING ENZYME / MESO-A2PM-ADDING ENZYME / UDP-N- ACETYLMURAMYL-TRIPEPTIDE SYNTHETASE / UDP-MURNAC-TRIPEPTIDE SYNTHETASE Mass: 55454.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)/PLYSS References: UniProt: P65477, UniProt: P9WJL3*PLUS, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-UAG / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE Mass: 879.608 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₈H₄₃N₅O₂₃P₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.4 % / Description: NONE
Crystal grow	pH: 8.5 / Details: 0.35 M MGCL2, 0.1 M TRIS PH 8.5, 16% PEG 8000.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
Detector	Type: ADSC CCD / Detector: CCD / Date: Dec 3, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 3→74.8 Å / Num. obs: 31925 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shell	Resolution: 3→3.16 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 95.9

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0077	refinement
MOSFLM		data reduction
SCALA		data scaling
SCALA		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WTZ

2wtz

Resolution: 3→76.3 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.867 / SU B: 46.79 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.546 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.258	1598	4.9 %	RANDOM
R_work	0.189	-	-	-
obs	0.193	30876	95.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 61.12 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.56 Å²	-1.27 Å²	-1.27 Å²
2-	-	-0.42 Å²	0.63 Å²
3-	-	-	-1.88 Å²

Refinement step

Cycle: LAST / Resolution: 3→76.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14123	0	350	4	14477

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	14731
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.846	1.994	20151
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.771	5	1976
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.931	22.481	540
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.153	15	1991
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.153	15	141
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	2452
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	11169
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.499	1.5	9709
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.926	2	15385
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.571	3	4899
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.608	4.5	4577
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	2	A	1336	tight positional	0.08	0.05
1	1	B	1336	tight positional	0.06	0.05
1	4	C	1336	tight positional	0.06	0.05
1	3	D	1336	tight positional	0.07	0.05
2	2	A	1027	tight positional	0.05	0.05
2	1	B	1027	tight positional	0.05	0.05
1	2	A	991	medium positional	0.08	0.5
1	1	B	991	medium positional	0.06	0.5
1	4	C	991	medium positional	0.06	0.5
1	3	D	991	medium positional	0.07	0.5
3	2	A	88	medium positional	0.28	0.5
3	1	B	88	medium positional	0.32	0.5
3	3	C	88	medium positional	0.3	0.5
3	4	D	88	medium positional	0.35	0.5
1	2	A	1336	tight thermal	2.44
1	1	B	1336	tight thermal	2.52
1	4	C	1336	tight thermal	2.78
1	3	D	1336	tight thermal	2.65
2	2	A	1027	tight thermal	2.23
2	1	B	1027	tight thermal	2.23
1	2	A	991	medium thermal	3.29
1	1	B	991	medium thermal	3.1
1	4	C	991	medium thermal	3.27
1	3	D	991	medium thermal	2.94
3	2	A	88	medium thermal	3.62
3	1	B	88	medium thermal	7.78
3	3	C	88	medium thermal	4.65
3	4	D	88	medium thermal	6.27

LS refinement shell

Resolution: 3→3.08 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.373	113	-
R_work	0.23	2286	-
obs	-	-	95.92 %

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	7.0048	-1.0878	1.7253	7.7704	1.0127	8.8993	-0.0931	-0.2971	0.1085	-0.2613	-0.0563	-0.7513	-0.1239	0.6964	0.1494	0.014	-0.0183	0.0204	0.272	0.0523	0.1053	27.46	-5.346	-1.37
2	5.5388	1.6027	-0.6931	7.3502	-0.8672	8.7146	0.0298	0.5415	-0.3013	0.0493	-0.0707	-1.0346	-0.1065	0.4381	0.0409	0.0123	0.0249	0.0246	0.2258	0.0498	0.2497	27.322	-23.611	20.754
3	7.6027	1.1033	-0.7068	7.9238	0.2883	9.2897	-0.0484	0.3646	-0.3602	0.8057	0.3448	0.7216	1.2515	-1.1276	-0.2964	0.4645	-0.2007	-0.0027	0.2431	0.1354	0.3209	-4.502	22.449	44.249
4	2.8009	-1.0015	1.0498	6.6937	-0.7941	11.9813	0.0561	-0.3898	0.2878	-0.3823	0.2416	0.7669	-0.9732	-0.8388	-0.2977	0.3703	0.2078	0.1787	0.249	0.1041	0.3503	-4.384	-2.24	57.247
5	6.9759	-1.4622	2.0036	3.0847	-0.7593	3.3985	0.0859	-0.1644	-0.2096	-0.1536	0.1681	0.6923	0.1951	-0.3463	-0.2539	0.2173	-0.0466	-0.0793	0.2204	0.0647	0.1935	-4.074	-3.134	-7.755
6	7.7993	1.4914	-3.2621	2.1613	-0.0983	3.7644	-0.03	0.0572	0.0894	-0.029	-0.0115	0.2393	-0.2742	-0.3131	0.0415	0.1449	0.0651	-0.0078	0.1927	0.0035	0.0522	-2.314	-23.51	31.621
7	6.784	0.6634	-0.0587	3.8804	-0.902	2.9168	-0.3246	-0.146	0.2955	0.2815	-0.002	-0.531	0.1122	0.3692	0.3266	0.3099	0.0625	-0.171	0.0989	-0.0387	0.2899	26.157	29.445	44.209
8	5.1817	-1.8657	0.8657	2.9302	0.3201	3.236	-0.0916	-0.0454	-0.0715	0.1053	0.113	-0.2551	-0.3294	0.3204	-0.0215	0.2678	-0.1305	0.0736	0.1125	-0.0451	0.213	25.485	-11.185	52.441
9	10.9656	-1.8633	0.0079	4.2417	-0.7022	6.7592	0.4211	0.3115	0.9162	-0.4021	-0.0915	-0.4766	-0.5434	0.164	-0.3296	0.4672	0.0774	0.2484	0.1659	-0.0251	0.46	-14.001	5.03	15.352
10	8.693	2.0654	-0.132	7.5348	-2.3755	8.8094	0.1185	-0.3959	-0.6769	-0.0781	-0.3271	-0.3751	0.443	0.3999	0.2086	0.3353	-0.0177	-0.0942	0.2356	0.0488	0.1828	-14.984	-31.793	9.383
11	9.9094	-0.1087	-2.2804	5.0268	0.8212	6.5226	0.165	0.3806	0.563	-0.3392	0.2211	0.2738	-0.3582	-0.2427	-0.386	0.3813	0.1124	0.1009	0.4439	0.0623	0.2598	35.563	11.668	26.621
12	9.463	-0.8029	6.4844	6.9895	-2.2038	13.4296	0.5427	-0.7399	-0.4916	-0.8396	-0.0785	0.1879	1.8666	-1.027	-0.4642	0.6016	-0.1886	-0.0293	0.3199	-0.0567	0.2224	39.196	4.887	68.722

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 139
2	X-RAY DIFFRACTION	2	B	26 - 139
3	X-RAY DIFFRACTION	3	C	26 - 139
4	X-RAY DIFFRACTION	4	D	26 - 139
5	X-RAY DIFFRACTION	5	A	140 - 379
6	X-RAY DIFFRACTION	5	A	1533 - 1535
7	X-RAY DIFFRACTION	6	B	140 - 379
8	X-RAY DIFFRACTION	6	B	1533 - 1537
9	X-RAY DIFFRACTION	7	C	140 - 379
10	X-RAY DIFFRACTION	7	C	1533 - 1536
11	X-RAY DIFFRACTION	8	D	140 - 379
12	X-RAY DIFFRACTION	8	D	1533 - 1537
13	X-RAY DIFFRACTION	9	A	380 - 533
14	X-RAY DIFFRACTION	10	B	380 - 533
15	X-RAY DIFFRACTION	11	C	380 - 533
16	X-RAY DIFFRACTION	12	D	380 - 533

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About Yorodumi

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Yorodumi