PDB-9o8y: Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate...

ID or keywords:

Entry

Database: PDB / ID: 9o8y

Title

Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) from Bordetella pertussis (succinyl-CoA bound)

Components

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / dapD / Bordetella pertussis

Function / homology

Function and homology information

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / nucleotidyltransferase activity / cytoplasm
Similarity search - Function

Biological species

Bordetella pertussis Tohama I (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (dapD) from Bordetella pertussis (succinyl-CoA bound)
Authors: Ung, A.R. / Lovell, S. / Cooper, A. / Battaile, K.P.

History

Deposition	Apr 17, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9o8y.cif.gz	321.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9o8y.ent.gz		Display	PDB format
PDBx/mmJSON format	9o8y.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/o8/9o8y ftp://data.pdbj.org/pub/pdb/validation_reports/o8/9o8y	HTTPS FTP

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Related structure data

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	#165 - Sep 2013 Designed Protein Cages similarity (3) #49 - Jan 2004 Carbonic Anhydrase similarity (3) #39 - Mar 2003 lac Repressor similarity (4)

Deposited unit

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

B: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

C: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

hetero molecules

90.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	86.264, 88.645, 117.291
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / Tetrahydrodipicolinate N-succinyltransferase / THDP succinyltransferase / THP succinyltransferase / ...Tetrahydrodipicolinate N-succinyltransferase / THDP succinyltransferase / THP succinyltransferase / Tetrahydropicolinate succinylase Mass: 29966.992 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria) Gene: dapD, BP1764 / Plasmid: BopeA.00002.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A4U8, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SCA / SUCCINYL-COENZYME A Mass: 867.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₅H₄₀N₇O₁₉P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.49 Å³/Da / Density % sol: 50.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Proplex B8: 15% w/v PEG 4000, 0.1 M sodium citrate pH 5.0, 0.1 M magnesium chloride. BopeA.00002.a.B2.PW39337 at 16.9 mg/mL. 2mM succinyl-CoA added prior to crystallization. Bound in one ...Details: Proplex B8: 15% w/v PEG 4000, 0.1 M sodium citrate pH 5.0, 0.1 M magnesium chloride. BopeA.00002.a.B2.PW39337 at 16.9 mg/mL. 2mM succinyl-CoA added prior to crystallization. Bound in one subunit only. plate 19707 A1 drop 1, Puck: PSL1209, Cryo: 80% crystallant + 20% PEG 200.

Crystal

Density Matthews: 2.49 Å³/Da / Density % sol: 50.68 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Proplex B8: 15% w/v PEG 4000, 0.1 M sodium citrate pH 5.0, 0.1 M magnesium chloride. BopeA.00002.a.B2.PW39337 at 16.9 mg/mL. 2mM succinyl-CoA added prior to crystallization. Bound in one ...

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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: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 15, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.45→48.91 Å / Num. obs: 159318 / % possible obs: 100 % / Redundancy: 13.5 % / CC_1/2: 1 / R_merge(I) obs: 0.083 / R_pim(I) all: 0.023 / R_rim(I) all: 0.086 / Χ²: 0.99 / Net I/σ(I): 17.2 / Num. measured all: 2145348
Reflection shell	Resolution: 1.45→1.47 Å / % possible obs: 100 % / Redundancy: 14 % / R_merge(I) obs: 1.735 / Num. measured all: 109008 / Num. unique obs: 7804 / CC_1/2: 0.415 / R_pim(I) all: 0.476 / R_rim(I) all: 1.8 / Χ²: 0.96 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	dev_5660	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→48.91 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1824	7957	5 %
R_work	0.1593	-	-
obs	0.1605	159181	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→48.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5791	0	54	686	6531

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6035
X-RAY DIFFRACTION	f_angle_d	0.961	8246
X-RAY DIFFRACTION	f_dihedral_angle_d	13.834	2183
X-RAY DIFFRACTION	f_chiral_restr	0.082	956
X-RAY DIFFRACTION	f_plane_restr	0.009	1073

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 (%)
1.45-1.47	0.3403	280	0.3176	4981	X-RAY DIFFRACTION	100
1.47-1.48	0.3256	264	0.294	4995	X-RAY DIFFRACTION	100
1.48-1.5	0.292	248	0.2797	5010	X-RAY DIFFRACTION	100
1.5-1.52	0.2733	240	0.2495	4994	X-RAY DIFFRACTION	100
1.52-1.54	0.2718	255	0.2429	5022	X-RAY DIFFRACTION	100
1.54-1.56	0.2516	284	0.2272	4966	X-RAY DIFFRACTION	100
1.56-1.58	0.2294	291	0.2187	4982	X-RAY DIFFRACTION	100
1.58-1.61	0.2203	275	0.2131	4985	X-RAY DIFFRACTION	100
1.61-1.63	0.2359	236	0.2229	5020	X-RAY DIFFRACTION	100
1.63-1.66	0.2665	271	0.2334	4992	X-RAY DIFFRACTION	100
1.66-1.69	0.2477	243	0.2168	5054	X-RAY DIFFRACTION	100
1.69-1.72	0.2252	256	0.1925	4964	X-RAY DIFFRACTION	100
1.72-1.75	0.2064	285	0.1796	4996	X-RAY DIFFRACTION	100
1.75-1.79	0.1941	280	0.1655	4989	X-RAY DIFFRACTION	100
1.79-1.83	0.177	239	0.1536	5050	X-RAY DIFFRACTION	100
1.83-1.87	0.1735	264	0.1424	5026	X-RAY DIFFRACTION	100
1.87-1.92	0.1789	275	0.1479	5014	X-RAY DIFFRACTION	100
1.92-1.97	0.1651	276	0.1477	5019	X-RAY DIFFRACTION	100
1.97-2.03	0.1766	271	0.1537	5029	X-RAY DIFFRACTION	100
2.03-2.09	0.1705	271	0.1505	4993	X-RAY DIFFRACTION	100
2.09-2.17	0.1739	244	0.1315	5086	X-RAY DIFFRACTION	100
2.17-2.25	0.1405	315	0.1303	4987	X-RAY DIFFRACTION	100
2.25-2.36	0.1622	261	0.1323	5037	X-RAY DIFFRACTION	100
2.36-2.48	0.1533	256	0.1383	5088	X-RAY DIFFRACTION	100
2.48-2.63	0.1678	271	0.1436	5067	X-RAY DIFFRACTION	100
2.63-2.84	0.1812	274	0.1522	5063	X-RAY DIFFRACTION	100
2.84-3.12	0.1678	250	0.1467	5105	X-RAY DIFFRACTION	100
3.12-3.58	0.1799	243	0.1545	5164	X-RAY DIFFRACTION	100
3.58-4.5	0.1539	273	0.1333	5186	X-RAY DIFFRACTION	100
4.5-48.91	0.1899	266	0.1701	5360	X-RAY DIFFRACTION	99

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	0.2713	-0.0108	0.1464	0.0015	-0.039	0.4742	0.0667	-0.252	-0.0398	0.235	-0.0739	-0.1099	-0.045	0.2306	-0.064	0.8626	-0.253	-0.4317	0.5299	0.0925	0.1649	-12.5991	8.9613	1.9453
2	4.7759	-0.3971	3.7743	0.0429	-0.1481	6.3187	0.067	-0.2159	-0.0678	0.4468	-0.1073	-0.636	0.097	0.9385	-0.29	0.4316	-0.0033	-0.2205	0.402	0.084	0.4436	-8.7002	4.957	-8.829
3	2.5586	-0.3936	2.0345	0.905	0.8979	4.2159	0.1788	-0.3288	-0.3003	0.6059	-0.1049	0.0176	0.3799	-0.0912	-0.1087	0.481	-0.0518	-0.0695	0.2225	0.0751	0.1697	-21.9868	4.1054	-9.921
4	2.0968	-0.7108	1.4701	3.6068	-0.4038	1.0473	-0.0367	-0.0956	0.1185	0.2852	-0.0388	-0.6374	-0.1753	0.0306	0.0958	0.1422	0.0086	-0.0498	0.2028	-0.0126	0.2326	-6.1901	19.4562	-18.7494
5	4.8333	-1.1623	1.7753	5.1179	-3.5527	3.2502	0.0583	0.1782	-0.3604	-0.2605	0.0393	-0.2769	0.2121	0.175	-0.0983	0.1219	0.0083	0.0125	0.1553	-0.0438	0.1727	-9.894	7.944	-31.0013
6	2.2296	0.28	-0.5399	4.6172	-0.2634	2.6004	0.0007	0.0451	-0.2198	0.0259	0.0424	-0.137	0.1294	0.0964	-0.0616	0.082	0.0204	-0.0006	0.1325	-0.0064	0.1034	-18.5867	8.9771	-26.6836
7	2.3004	-0.0374	0.8054	1.8585	-0.02	1.4457	0.0021	-0.1642	0.0051	0.1831	-0.0102	0.1758	0.0558	-0.0186	0.0113	0.1318	-0.0079	0.0257	0.1251	0.0103	0.1064	-32.1447	10.7149	-22.6788
8	1.8846	-0.6736	-0.2821	0.3935	0.1128	0.7502	0.0134	-0.1821	0.0172	0.0623	-0.0361	0.4965	0.0131	-0.146	0.0194	0.1301	-0.0257	0.0394	0.1752	-0.0203	0.3113	-48.4599	14.3817	-23.8407
9	2.2098	-1.9479	-0.4872	7.1223	3.028	2.4642	0.036	0.2232	-0.0034	-0.5356	0.0556	0.1493	-0.0958	0.1191	-0.0545	0.1836	-0.0412	-0.0106	0.2022	0.0146	0.2591	-41.347	8.7244	-34.5558
10	6.1695	-1.9969	-3.0552	6.1013	2.2506	6.7499	0.1587	0.3889	0.7765	-0.2234	0.0759	0.0526	-0.3065	-0.0278	-0.2307	0.1436	-0.0307	-0.0156	0.1702	0.0374	0.3556	-10.7707	56.6364	-34.4199
11	5.7645	5.841	-5.1043	6.7743	-6.2638	8.7011	0.0564	-0.1491	0.1193	0.1252	-0.226	-0.3727	-0.1268	0.429	0.2059	0.1034	-0.0069	-0.0105	0.1611	-0.0192	0.2845	-6.6239	49.8184	-25.8092
12	5.122	0.2731	-2.0249	3.1708	-0.6616	4.2864	0.1161	-0.0271	0.5301	0.3513	0.0016	0.2616	-0.2086	-0.3486	-0.1376	0.1512	-0.0076	0.0025	0.136	-0.0454	0.2873	-19.8538	49.7115	-23.2441
13	1.6075	1.0796	-0.3263	2.8416	-0.6364	4.9266	-0.0691	0.0068	-0.0448	-0.2282	0.0828	-0.4616	0.2341	0.2036	-0.0128	0.1203	-0.0076	0.0459	0.191	-0.0218	0.2891	-5.7135	33.6254	-32.7309
14	5.0801	2.3001	0.1944	3.3282	0.4258	1.4533	0.1111	-0.5255	0.0829	0.3886	-0.0917	-0.4391	0.1017	0.1133	-0.0265	0.1474	0.0275	-0.0504	0.2115	-0.043	0.2081	-8.9047	28.96	-16.3084
15	2.0562	0.1142	-0.3127	2.684	-0.0122	1.1993	0.0017	-0.1418	0.1977	0.193	0.0438	-0.0394	-0.036	0.0534	-0.0274	0.1069	0.002	-0.0063	0.1413	-0.0309	0.122	-21.6125	35.8921	-20.7366
16	4.5229	-0.6804	0.4451	1.0245	-0.4689	1.5293	-0.033	-0.0442	0.1877	0.123	-0.0369	0.3561	-0.0412	-0.0526	0.0621	0.1232	-0.0034	0.032	0.1368	-0.0358	0.2258	-38.6404	35.4818	-21.3746
17	6.6105	0.7904	4.7135	2.3382	0.5442	7.1578	-0.0409	-0.3109	0.0004	-0.0125	-0.0001	0.5256	-0.2272	-0.3628	-0.0182	0.1151	0.0188	0.0313	0.1313	-0.0239	0.3503	-47.8923	30.9393	-24.4858
18	0.4548	0.6413	0.2278	1.435	0.011	2.0701	0.0023	0.4037	-0.16	-0.6818	0.0249	-0.4289	-0.0267	0.0536	0.0103	0.5365	-0.0802	0.1337	0.361	-0.1019	0.216	-15.1983	10.0897	-56.3342
19	1.336	-0.1298	0.3987	1.417	0.0348	1.0456	-0.0417	0.2381	0.0978	-0.3844	0.0929	-0.2526	-0.0376	0.0977	-0.0252	0.2006	-0.0297	0.0621	0.1919	-0.0049	0.126	-14.2307	24.0831	-41.7721
20	2.8753	-0.2522	-1.0299	0.8051	0.2353	1.5729	-0.1259	0.2859	-0.004	-0.3635	0.0309	0.3702	0.0067	-0.0721	0.0701	0.2341	-0.0237	-0.1046	0.1626	0.0191	0.1914	-39.0955	24.0357	-42.9878

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 41 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 42 through 69 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 95 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 96 through 112 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 113 through 144 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 145 through 217 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 218 through 246 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 247 through 268 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 25 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 26 through 41 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 42 through 69 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 70 through 95 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 96 through 112 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 113 through 182 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 183 through 231 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 232 through 257 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1 through 69 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 70 through 162 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 163 through 257 )

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Yorodumi