PDB-9bt3: Crystal structure of Chorismate Mutase from Mycobacterium tubercu...

ID or keywords:

Entry

Database: PDB / ID: 9bt3

Title

Crystal structure of Chorismate Mutase from Mycobacterium tuberculosis in complex with the cyclic peptide inhibitor L2.1 (triclinic form)

Components

Peptide L2.1
Secreted chorismate mutase

Keywords

ISOMERASE / Chorismate Mutase / Mycobacterium tuberculosis / cyclic peptide inhibitor

Function / homology

Function and homology information

salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / extracellular region
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Liu, L. / Lovell, S. / Battaile, K.P. / Inglese, J.

Funding support

United States, 1items

Citation

Journal: Acs Infect Dis. / Year: 2025
Title: Active- and Allosteric-Site Cyclic Peptide Inhibitors of Secreted M. tuberculosis Chorismate Mutase.
Authors: van Neer, R.H.P. / Dranchak, P.K. / Aitha, M. / Liu, L. / Carlson, E.K. / Jacobsen, I.E. / Battaile, K. / Fang, Y. / Tao, D. / Rai, G. / Padia, J. / Lovell, S. / Suga, H. / Inglese, J.

History

Deposition	May 14, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 26, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bt3.cif.gz	569.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9bt3.ent.gz	470.5 KB	Display	PDB format
PDBx/mmJSON format	9bt3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bt/9bt3 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/9bt3	HTTPS FTP

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Related structure data

Related structure data	9bt6C 9bt7C C: citing same article (ref.)
Similar structure data	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
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (1)

Deposited unit

A: Secreted chorismate mutase

B: Secreted chorismate mutase

C: Secreted chorismate mutase

D: Secreted chorismate mutase

E: Secreted chorismate mutase

F: Secreted chorismate mutase

G: Secreted chorismate mutase

H: Secreted chorismate mutase

a: Peptide L2.1

b: Peptide L2.1

c: Peptide L2.1

d: Peptide L2.1

e: Peptide L2.1

f: Peptide L2.1

g: Peptide L2.1

h: Peptide L2.1

hetero molecules

200 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Secreted chorismate mutase

a: Peptide L2.1

hetero molecules

defined by author&software
Evidence: gel filtration
25.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Secreted chorismate mutase

b: Peptide L2.1

hetero molecules

defined by author&software
25.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Secreted chorismate mutase

c: Peptide L2.1

hetero molecules

defined by author&software
25.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Secreted chorismate mutase

d: Peptide L2.1

hetero molecules

defined by author&software
25.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Secreted chorismate mutase

e: Peptide L2.1

hetero molecules

defined by author&software
24.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Secreted chorismate mutase

f: Peptide L2.1

hetero molecules

defined by author&software
24.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Secreted chorismate mutase

g: Peptide L2.1

hetero molecules

defined by author&software
24.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Secreted chorismate mutase

h: Peptide L2.1

hetero molecules

defined by author&software
24.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.940, 73.401, 117.862
Angle α, β, γ (deg.)	74.75, 82.21, 77.39
Int Tables number	1
Space group name H-M	P1

#1: Protein	Secreted chorismate mutase / CM / MtCM Mass: 22973.375 Da / Num. of mol.: 8 / Fragment: D34-A199 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis* (bacteria) / Gene: Rv1885c / Plasmid: pET21a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIB9, chorismate mutase
#2: Protein/peptide	Peptide L2.1 Mass: 1766.086 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.12 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: JCSG+ E9: 1.6 M magnesium sulfate, 100 mM MES pH 6.5, chorismate mutase at 10 mg/mL. plate 12876, well E9 drop 2. Puck: PSL-0601, Cryo: 2.5M lithium sulfate.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 10, 2023
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.5→113.32 Å / Num. obs: 63077 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC_1/2: 0.986 / R_merge(I) obs: 0.186 / R_pim(I) all: 0.115 / R_rim(I) all: 0.219 / Χ²: 0.96 / Net I/σ(I): 5.7 / Num. measured all: 222497
Reflection shell	Resolution: 2.5→2.56 Å / % possible obs: 97.7 % / Redundancy: 3.6 % / R_merge(I) obs: 1.282 / Num. measured all: 17014 / Num. unique obs: 4671 / CC_1/2: 0.475 / R_pim(I) all: 0.779 / R_rim(I) all: 1.503 / Χ²: 0.98 / Net I/σ(I) obs: 1.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→38.72 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2747	3066	4.87 %
R_work	0.2285	-	-
obs	0.2308	63007	98.22 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→38.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11160	0	115	90	11365

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11508
X-RAY DIFFRACTION	f_angle_d	1.009	15684
X-RAY DIFFRACTION	f_dihedral_angle_d	14.349	4226
X-RAY DIFFRACTION	f_chiral_restr	0.048	1700
X-RAY DIFFRACTION	f_plane_restr	0.011	2038

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.54	0.4251	143	0.3588	2747	X-RAY DIFFRACTION	97
2.54-2.58	0.3633	163	0.3139	2674	X-RAY DIFFRACTION	98
2.58-2.63	0.3721	145	0.3046	2691	X-RAY DIFFRACTION	98
2.63-2.67	0.364	141	0.2927	2721	X-RAY DIFFRACTION	98
2.67-2.72	0.3436	129	0.2869	2728	X-RAY DIFFRACTION	98
2.72-2.78	0.3444	149	0.2956	2691	X-RAY DIFFRACTION	98
2.78-2.84	0.3389	140	0.2954	2704	X-RAY DIFFRACTION	98
2.84-2.91	0.3242	120	0.2722	2741	X-RAY DIFFRACTION	98
2.91-2.98	0.318	140	0.2641	2757	X-RAY DIFFRACTION	98
2.98-3.06	0.3275	147	0.2657	2686	X-RAY DIFFRACTION	98
3.06-3.15	0.3014	125	0.2608	2750	X-RAY DIFFRACTION	98
3.15-3.25	0.2894	141	0.2652	2721	X-RAY DIFFRACTION	98
3.25-3.37	0.2973	112	0.253	2778	X-RAY DIFFRACTION	98
3.37-3.5	0.2622	133	0.226	2708	X-RAY DIFFRACTION	98
3.5-3.66	0.2634	173	0.2166	2696	X-RAY DIFFRACTION	98
3.66-3.85	0.2988	123	0.2108	2722	X-RAY DIFFRACTION	98
3.85-4.1	0.231	131	0.1869	2713	X-RAY DIFFRACTION	98
4.1-4.41	0.2332	145	0.1819	2732	X-RAY DIFFRACTION	99
4.41-4.85	0.2066	134	0.1726	2783	X-RAY DIFFRACTION	99
4.85-5.55	0.2315	150	0.1889	2732	X-RAY DIFFRACTION	99
5.56-6.99	0.287	139	0.2409	2759	X-RAY DIFFRACTION	99
6.99-38.72	0.2034	143	0.1724	2707	X-RAY DIFFRACTION	98

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	1.8432	0.4666	-0.447	2.0038	-0.1848	1.9121	0.1519	0.1936	0.2666	-0.0935	0.0621	-0.2336	-0.1837	0.1029	-0.2217	0.3796	0.0133	0.06	0.4653	0.0531	0.3147	13.8285	-7.0202	-33.03
2	2.7526	-0.3158	0.0215	3.1468	-0.195	1.1038	-0.1287	0.3019	0.0514	-0.7098	0.2092	0.1573	-0.051	-0.4351	-0.1329	0.4382	-0.024	-0.029	0.5547	0.0785	0.1763	7.9159	-19.5383	-39.4394
3	1.8888	-0.8756	-0.5941	1.0702	0.1716	1.7132	0.0048	0.1922	0.1035	-0.0123	-0.0188	0.0561	0.022	-0.0092	0.0186	0.2558	-0.0105	0.0229	0.2663	0.0146	0.2559	-7.7326	-17.2918	-7.9277
4	5.0028	-1.9024	0.2713	5.5798	0.4626	4.1926	-0.2646	0.4769	-0.1702	0.2621	-0.0997	-0.1001	0.4725	0.4017	0.3621	0.3076	0.03	0.0028	0.2643	-0.0165	0.2738	-1.9386	-30.7206	-12.0796
5	2.9106	0.9574	1.0731	1.7722	-0.1167	2.3684	0.09	0.139	-0.1205	-0.1168	-0.0893	0.1419	0.0418	-0.0285	0.009	0.3111	0.0273	-0.0038	0.25	-0.0278	0.2388	7.9884	20.2764	15.0561
6	5.0166	-0.0876	-0.1326	2.6557	-0.4876	1.1047	-0.0261	0.1094	-0.3636	-0.3056	-0.0872	0.1899	-0.2947	0.0534	0.0646	0.3972	-0.069	-0.0138	0.2446	-0.0415	0.1628	13.9354	33.8998	18.4995
7	3.097	-1.246	0.3634	2.1217	-0.7066	1.94	0.1415	-0.1924	-0.2229	0.0379	0.017	-0.1306	0.2246	0.0271	-0.1521	0.331	-0.004	-0.0455	0.3877	0.056	0.3438	29.6499	11.0502	40.3717
8	2.726	0.0146	1.0795	5.3724	-0.5609	4.2697	-0.3107	0.1952	0.1185	0.5344	0.3896	-0.0148	-0.1649	-0.3422	0.0108	0.3791	-0.0222	0.0052	0.4585	-0.0364	0.2547	23.8003	23.7667	46.4615
9	1.8348	0.807	-0.1576	3.5148	-0.3103	1.1987	-0.0045	-0.149	0.227	0.196	0.0262	0.0166	-0.1486	0.0129	-0.0151	0.2792	-0.0201	0.0249	0.2171	-0.0418	0.2426	19.3618	-18.7055	10.6716
10	5.1413	4.7615	-2.4208	6.2725	-2.4902	1.6006	0.1605	-0.1193	0.5366	0.2731	0.1015	0.633	-0.2917	-0.1951	-0.2311	0.3558	-0.0383	0.0612	0.3724	0.0422	0.4607	6.1333	-24.5942	13.8034
11	1.4631	-0.8641	0.9924	2.2655	0.0096	2.2213	0.5543	0.3616	-0.578	-0.2763	-0.1228	0.1165	0.6305	0.2789	-0.2186	0.4959	0.0831	-0.1769	0.3499	-0.0977	0.4559	19.756	-49.6391	-4.4941
12	5.0991	-2.6121	0.5035	5.6695	-2.6099	3.6323	0.8076	0.0392	-0.4919	-0.1594	0.0991	0.5166	0.3513	-0.3471	-0.8427	0.4905	0.0257	-0.114	0.4221	-0.0236	0.4947	6.5067	-43.994	-7.6853
13	3.2438	-0.0121	1.678	2.5327	0.9649	2.8165	0.3909	0.1642	-0.6868	-0.0328	-0.0154	0.0654	0.4096	0.165	-0.3487	0.3962	0.044	-0.0894	0.4367	0.0421	0.4291	-13.7503	-28.562	-57.7786
14	4.5905	1.7308	4.7086	1.9397	2.0792	5.5101	0.4035	0.2648	-0.5688	-0.0509	0.3158	-0.1028	0.073	0.4152	-0.6394	0.3374	0.0519	-0.0483	0.4317	-0.0382	0.381	-0.4821	-26.3205	-51.5937
15	2.3262	0.3085	-1.5296	3.1507	0.8565	3.6098	0.3263	-0.2143	0.5273	0.11	0.0352	0.2796	-0.3129	0.206	-0.3523	0.3428	-0.0085	0.1209	0.4673	0.0448	0.443	-13.7671	4.6859	-48.4319
16	6.4903	-1.9729	-5.7648	1.7507	1.7893	7.1186	0.368	-0.0783	0.6644	-0.1359	0.514	-0.1225	-0.0202	0.7405	-0.8823	0.3719	-0.0311	0.0044	0.5714	0.0222	0.3984	-0.5461	2.5174	-54.6546

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain a
3	X-RAY DIFFRACTION	3	chain B
4	X-RAY DIFFRACTION	4	chain b
5	X-RAY DIFFRACTION	5	chain C
6	X-RAY DIFFRACTION	6	chain c
7	X-RAY DIFFRACTION	7	chain D
8	X-RAY DIFFRACTION	8	chain d
9	X-RAY DIFFRACTION	9	chain E
10	X-RAY DIFFRACTION	10	chain e
11	X-RAY DIFFRACTION	11	chain F
12	X-RAY DIFFRACTION	12	chain f
13	X-RAY DIFFRACTION	13	chain G
14	X-RAY DIFFRACTION	14	chain g
15	X-RAY DIFFRACTION	15	chain H
16	X-RAY DIFFRACTION	16	chain h

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