PDB-3n8k: Type II dehydroquinase from Mycobacterium tuberculosis complexed ...

ID or keywords:

Entry

Database: PDB / ID: 3n8k

Title

Type II dehydroquinase from Mycobacterium tuberculosis complexed with citrazinic acid

Components

3-dehydroquinate dehydratase

Keywords

LYASE / DEHYDRATASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / tuberculosis / drug target / citrazinic acid / Structural Genomics / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Snee, W.C. / Palaninathan, S.K. / Sacchettini, J.C. / Dias, M.V.B. / Bromfield, K.M. / Payne, R. / Ciulli, A. / Howard, N.I. / Abell, C. / Blundell, T.L. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: Biochem.J. / Year: 2011
Title: Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis.
Authors: Dias, M.V. / Snee, W.C. / Bromfield, K.M. / Payne, R.J. / Palaninathan, S.K. / Ciulli, A. / Howard, N.I. / Abell, C. / Sacchettini, J.C. / Blundell, T.L.

History

Deposition	May 28, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3n8k.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb3n8k.ent.gz	1.1 MB	Display	PDB format
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Validation report

Summary document	3n8k_validation.pdf.gz	685.9 KB	Display	wwPDB validaton report
Full document	3n8k_full_validation.pdf.gz	749.6 KB	Display
Data in XML	3n8k_validation.xml.gz	136.1 KB	Display
Data in CIF	3n8k_validation.cif.gz	178.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n8/3n8k ftp://data.pdbj.org/pub/pdb/validation_reports/n8/3n8k	HTTPS FTP

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Related structure data

Related structure data	3n59SC 3n76C 3n7aC 3n86C 3n87C 3n8nC 1h05 1h0r 1h0s 2dhq S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4b6p-1 4ki7-1 4cl0-1 4kiu-1 4ki7-2 2xb8-1 3n7a-1 6sme-1 3n7a-2 4kiu-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
Related items in Molecule of the Month	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (8)

Deposited unit

A: 3-dehydroquinate dehydratase

B: 3-dehydroquinate dehydratase

C: 3-dehydroquinate dehydratase

D: 3-dehydroquinate dehydratase

E: 3-dehydroquinate dehydratase

F: 3-dehydroquinate dehydratase

G: 3-dehydroquinate dehydratase

H: 3-dehydroquinate dehydratase

I: 3-dehydroquinate dehydratase

J: 3-dehydroquinate dehydratase

K: 3-dehydroquinate dehydratase

L: 3-dehydroquinate dehydratase

M: 3-dehydroquinate dehydratase

N: 3-dehydroquinate dehydratase

O: 3-dehydroquinate dehydratase

P: 3-dehydroquinate dehydratase

Q: 3-dehydroquinate dehydratase

R: 3-dehydroquinate dehydratase

S: 3-dehydroquinate dehydratase

T: 3-dehydroquinate dehydratase

U: 3-dehydroquinate dehydratase

V: 3-dehydroquinate dehydratase

W: 3-dehydroquinate dehydratase

X: 3-dehydroquinate dehydratase

hetero molecules

452 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3-dehydroquinate dehydratase

B: 3-dehydroquinate dehydratase

C: 3-dehydroquinate dehydratase

D: 3-dehydroquinate dehydratase

E: 3-dehydroquinate dehydratase

F: 3-dehydroquinate dehydratase

G: 3-dehydroquinate dehydratase

H: 3-dehydroquinate dehydratase

I: 3-dehydroquinate dehydratase

J: 3-dehydroquinate dehydratase

K: 3-dehydroquinate dehydratase

L: 3-dehydroquinate dehydratase

hetero molecules

defined by author&software
226 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

M: 3-dehydroquinate dehydratase

N: 3-dehydroquinate dehydratase

O: 3-dehydroquinate dehydratase

P: 3-dehydroquinate dehydratase

Q: 3-dehydroquinate dehydratase

R: 3-dehydroquinate dehydratase

S: 3-dehydroquinate dehydratase

T: 3-dehydroquinate dehydratase

U: 3-dehydroquinate dehydratase

V: 3-dehydroquinate dehydratase

W: 3-dehydroquinate dehydratase

X: 3-dehydroquinate dehydratase

hetero molecules

defined by author&software
226 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.316, 137.208, 146.713
Angle α, β, γ (deg.)	90.00, 96.59, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	... 3-dehydroquinate dehydratase / 3-dehydroquinase / Type II DHQase Mass: 18649.947 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroD, aroQ, MT2612, MTCY159.19, Rv2537c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical	... ChemComp-D1X / 2,6-dioxo-1,2,3,6-tetrahydropyridine-4-carboxylic acid Mass: 155.108 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₆H₅NO₄
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1307 / 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: 2.15 Å³/Da / Density % sol: 42.83 %
Crystal grow	Temperature: 290 K / Method: microbatch Details: MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 ...Details: MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 mg/mL protein, 15% PEG monomethyl ether 2,000, 0.075 M KBr, 25 mM Tris, 50 mM NaCl, 0.5 mM DTT, 0.5 mM EDTA, pH 7.5 in microbatch plates covered with 5 mL Al s oil, Microbatch, temperature 290K

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.83 %

Crystal grow

Temperature: 290 K / Method: microbatch
Details: MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.77→50 Å / Num. all: 176635 / Num. obs: 176635 / % possible obs: 98.44 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MOLREP		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3N59

3n59

Resolution: 2.25→50 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.916 / SU B: 14.791 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23612	8851	5 %	RANDOM
R_work	0.20479	-	-	-
obs	0.20636	167784	98.43 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 43.441 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	0 Å²	0.21 Å²
2-	-	0.33 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25582	0	268	1307	27157

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.021	26285
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.881	1.97	35816
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.435	5	3375
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.252	23.371	1160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.404	15	4103
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.442	15	228
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	4218
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	20043
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.159	0.2	12675
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.29	0.2	17350
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.088	0.2	1820
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	0.15	0.2	65
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.077	0.2	27
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	0.117	1.5	16767
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.229	2	26718
X-RAY DIFFRACTION	r_scbond_it	0.362	3	9518
X-RAY DIFFRACTION	r_scangle_it	0.643	4.5	9093
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.307 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	616	-
R_work	0.257	11671	-
obs	-	-	93.16 %

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	2.5836	-0.0531	0.9293	2.1552	-0.0539	2.0253	-0.0463	-0.1687	-0.1701	0.0264	0.0206	0.0053	0.1547	-0.0505	0.0257	0.1033	-0.018	0.0266	0.0386	0.0408	0.059	-35.542	3.0675	-15.4879
2	2.4117	0.4611	0.0998	2.3398	0.2918	1.8645	-0.0347	0.2255	0.0476	-0.2443	0.0878	-0.0822	-0.1023	0.0201	-0.0531	0.0623	-0.0564	0.0282	0.1355	0.0375	0.0807	-20.9358	44.5889	-46.3801
3	2.1737	-0.597	-0.5273	1.9096	0.479	2.1933	0.0401	-0.1524	0.3247	-0.0025	-0.0214	-0.1947	-0.2374	0.1479	-0.0187	0.1069	-0.0617	0.0145	0.0808	-0.0278	0.2204	-12.4305	60.2113	-21.4916
4	1.7337	0.058	-0.0187	1.9003	0.3019	2.7835	-0.0072	-0.0137	0.1368	0.0477	0.0065	0.1841	-0.0244	-0.1497	0.0007	0.0005	-0.0002	0.0091	0.0658	-0.0387	0.0981	-62.3746	40.1054	-25.5181
5	1.7729	-0.0437	-0.0437	2.2333	-0.0804	2.4185	-0.0358	-0.0357	-0.0434	-0.0056	0.0167	-0.2463	0.0469	0.2061	0.0191	0.0065	-0.0197	0.0076	0.1166	0.0215	0.1752	-1.1901	32.447	-26.6325
6	1.863	0.4965	0.2066	2.2622	-0.3073	1.8018	-0.0382	0.1306	0.0956	-0.13	0.0275	-0.0122	0.0208	0.0554	0.0107	0.0158	-0.0152	-0.007	0.092	0.0226	0.0351	-42.4379	35.7171	-47.9618
7	2.6331	-0.8157	0.3678	2.0216	-0.2646	1.8902	0.0389	0.0405	-0.2031	-0.0238	-0.0995	0.1129	0.1864	-0.1294	0.0605	0.0575	-0.0271	0.0026	0.0463	-0.0296	0.0474	-50.9891	12.4051	-30.2445
8	2.4859	-0.2012	-0.2651	1.6677	-0.0227	1.8435	0.0318	-0.216	0.3399	0.0958	-0.03	-0.114	-0.252	0.112	-0.0018	0.1592	-0.073	0.0173	0.1171	-0.1242	0.1983	-28.234	63.6015	-4.5152
9	1.9572	0.2646	0.1889	1.9591	0.5796	2.7996	-0.0053	-0.0877	0.1942	0.1218	-0.0278	0.2365	-0.1046	-0.1258	0.0331	0.074	0.0068	0.0355	0.0775	-0.0949	0.1531	-56.0059	51.6744	-6.2155
10	1.5879	-0.2147	0.2814	2.9199	0.0327	1.2797	0.0456	-0.3597	0.0573	0.3396	-0.0148	0.0713	0.0247	0.0458	-0.0308	0.242	-0.0263	0.018	0.2273	-0.0739	0.0571	-36.1867	40.2351	13.4134
11	2.3188	0.7466	-0.3559	2.1732	-0.7884	2.7283	-0.0844	-0.1166	-0.2703	0.0619	-0.0311	-0.4404	0.1878	0.262	0.1155	0.0635	0.023	-0.0035	0.1259	0.0451	0.2264	-7.6886	14.6995	-12.6804
12	2.2218	0.1238	-0.2598	3.1173	0.384	1.5555	0.0799	-0.3965	-0.0229	0.3954	0.0105	-0.1171	0.0862	0.1157	-0.0903	0.2394	-0.0001	-0.0632	0.1927	0.0191	0.0216	-27.8078	18.7839	9.5193
13	1.9648	-0.057	-1.1944	1.3086	1.2688	4.2467	0.3706	0.0128	0.363	-0.0011	0.2955	-0.2067	-0.5483	0.2769	-0.6661	0.2821	0.0041	0.1883	0.1211	-0.1251	0.3526	-18.2621	136.2236	-47.231
14	2.1687	-1.011	-0.3949	2.3806	0.6749	3.4056	-0.3833	-0.2305	-0.2152	0.7137	0.3476	0.1495	1.3686	0.0394	0.0357	1.2559	0.2154	-0.063	0.2005	0.0849	0.1576	-20.353	82.6328	-47.2927
15	2.7492	-0.4092	-0.0839	1.7299	0.0371	3.6307	-0.4355	-0.5381	-0.1892	0.5427	0.4432	-0.2723	1.0316	0.9612	-0.0077	1.2021	0.8509	-0.3022	0.8815	-0.182	0.3311	9.691	80.6227	-45.0813
16	2.2313	0.0556	-0.5233	1.7354	0.0484	3.4414	0.0768	-0.0438	0.147	0.0227	0.2222	-0.0972	0.1873	0.0925	-0.299	0.0344	0.0258	-0.044	0.1139	-0.037	0.1016	-12.4996	108.7779	-85.3723
17	3.2675	0.5237	-0.7019	2.2176	0.4384	3.6222	-0.0201	-0.7193	0.005	0.782	0.4708	-0.217	1.1739	0.9623	-0.4507	1.1264	0.6391	-0.3921	0.7223	-0.193	0.2464	-6.186	97.3507	-24.966
18	2.2426	-0.7514	-0.4039	2.2011	0.2951	3.6171	-0.0896	0.0665	-0.1795	0.3099	0.0774	0.1332	0.953	-0.3893	0.0122	0.452	-0.0994	-0.0506	0.1668	0.0674	0.1123	-29.9951	94.8652	-64.7553
19	1.7274	-0.1631	-0.4134	2.2755	0.516	4.152	0.199	0.1451	0.3094	0.0727	0.131	0.0458	-0.302	-0.5155	-0.33	0.1277	0.1264	0.0911	0.1787	0.0668	0.188	-28.3161	125.1016	-65.3837
20	1.5744	-0.689	-0.8813	1.8037	-0.8176	3.4509	-0.2341	-0.6616	0.0112	0.497	0.463	-0.5657	0.7873	1.429	-0.2289	0.6871	0.7741	-0.4115	1.3075	-0.4681	0.5146	23.351	91.4536	-61.1712
21	3.2531	-0.4059	-1.2524	2.1201	1.067	3.5937	0.0311	-0.5281	0.4018	0.0254	0.5533	-0.4595	0.1305	0.8495	-0.5844	0.0344	0.1073	-0.0524	0.4746	-0.3373	0.3199	10.9094	107.8811	-83.7023
22	0.1941	0.4403	0.6381	5.0156	0.3566	3.4896	0.2231	-0.3895	0.3986	-0.1507	-0.0437	-1.5659	-0.1335	2.157	-0.1793	0.122	-0.0726	0.1047	2.2645	-0.9687	1.3852	25.524	121.8579	-61.1648
23	1.4603	1.1412	-0.0954	2.5818	-0.3438	3.3304	0.2158	-0.4936	0.2233	0.5227	0.4477	-0.099	0.4156	0.8888	-0.6635	0.4435	0.3138	-0.1769	0.861	-0.4886	0.4488	-3.7829	120.8592	-25.4891
24	2.0279	-1.0329	-1.2618	1.2113	0.6054	3.5948	0.3058	-0.6495	0.6435	0.0721	0.5592	-0.6784	-0.5953	1.5756	-0.8649	0.3083	-0.2629	0.1355	1.1934	-0.8625	0.8803	12.8495	135.907	-46.8585

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 144
2	X-RAY DIFFRACTION	2	B	3 - 144
3	X-RAY DIFFRACTION	3	C	2 - 143
4	X-RAY DIFFRACTION	4	D	2 - 144
5	X-RAY DIFFRACTION	5	E	2 - 144
6	X-RAY DIFFRACTION	6	F	3 - 143
7	X-RAY DIFFRACTION	7	G	2 - 144
8	X-RAY DIFFRACTION	8	H	3 - 143
9	X-RAY DIFFRACTION	9	I	3 - 143
10	X-RAY DIFFRACTION	10	J	3 - 143
11	X-RAY DIFFRACTION	11	K	3 - 143
12	X-RAY DIFFRACTION	12	L	3 - 143
13	X-RAY DIFFRACTION	13	M	-6 - 144
14	X-RAY DIFFRACTION	14	N	3 - 143
15	X-RAY DIFFRACTION	15	O	3 - 143
16	X-RAY DIFFRACTION	16	P	3 - 143
17	X-RAY DIFFRACTION	17	Q	3 - 143
18	X-RAY DIFFRACTION	18	R	3 - 143
19	X-RAY DIFFRACTION	19	S	3 - 143
20	X-RAY DIFFRACTION	20	T	3 - 143
21	X-RAY DIFFRACTION	21	U	3 - 143
22	X-RAY DIFFRACTION	22	V	3 - 143
23	X-RAY DIFFRACTION	23	W	3 - 143
24	X-RAY DIFFRACTION	24	X	3 - 143

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