PDB-3pb2: Characterisation of the first monomeric dihydrodipicolinate synth...

ID or keywords:

Entry

Database: PDB / ID: 3pb2

Title

Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals evolutionary insights

Components

Dihydrodipicolinate synthase

Keywords

LYASE /

TIM-Barrel

Function / homology

Function and homology information

4-hydroxy-tetrahydrodipicolinate synthase /

4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate /

cytosol
Similarity search - Function

Biological species

thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Pearce, F.G. / Dobson, R.C.J. / Jameson, G.B.

Citation

Journal: Biochim.Biophys.Acta / Year: 2011
Title: Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization.
Authors: Pearce, F.G. / Dobson, R.C. / Jameson, G.B. / Perugini, M.A. / Gerrard, J.A.

History

Deposition	Oct 20, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	3pb2.cif.gz	373.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3pb2.ent.gz	305.6 KB	Display	PDB format
PDBx/mmJSON format	3pb2.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/pb/3pb2 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/3pb2	HTTPS FTP

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Related structure data

Related structure data	3pb0C C: citing same article (ref.)
Similar structure data	6mqh-1 3ird-1 2ehh-d 3i7r-2 1yxc-1 4r53-d 1o5k-1 2yxg-d 5f1v-d 5j5d-1 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: Dihydrodipicolinate synthase

B: Dihydrodipicolinate synthase

C: Dihydrodipicolinate synthase

D: Dihydrodipicolinate synthase

E: Dihydrodipicolinate synthase

F: Dihydrodipicolinate synthase

hetero molecules

199 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dihydrodipicolinate synthase

B: Dihydrodipicolinate synthase

C: Dihydrodipicolinate synthase

E: Dihydrodipicolinate synthase

hetero molecules

defined by author
133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Dihydrodipicolinate synthase

F: Dihydrodipicolinate synthase

hetero molecules

D: Dihydrodipicolinate synthase

F: Dihydrodipicolinate synthase

hetero molecules

defined by author
132 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	192.200, 125.342, 78.428
Angle α, β, γ (deg.)	90.00, 103.54, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-741- HOH
2	1	D-854- HOH
3	1	F-843- HOH

#1: Protein	Dihydrodipicolinate synthase / / DHDPS Mass: 32885.672 Da / Num. of mol.: 6 / Mutation: R233A, R237A Source method: isolated from a genetically manipulated source Source: (gene. exp.) thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1K9, dihydrodipicolinate synthase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1073 / 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: 2.33 Å³/Da / Density % sol: 47.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 40% v/v PEG 300, 100mM phosphate-citrate buffer, pH 4.2, 0.02% (w/v) sodium azide, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95661 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2006
Radiation	Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95661 Å / Relative weight: 1
Reflection	Resolution: 1.9→33.259 Å / Num. obs: 143667 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
AMoRE		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→33.19 Å / SU ML: 0.25 / σ(F): 1.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2104	7115	5.02 %
R_work	0.1686	-	-
obs	0.1707	141790	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 61.761 Å² / k_sol: 0.381 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2365 Å²	-0 Å²	0.358 Å²
2-	-	-0.1659 Å²	-0 Å²
3-	-	-	0.4024 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→33.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13722	0	90	1073	14885

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	14088
X-RAY DIFFRACTION	f_angle_d	1.012	19126
X-RAY DIFFRACTION	f_dihedral_angle_d	12.903	5317
X-RAY DIFFRACTION	f_chiral_restr	0.068	2274
X-RAY DIFFRACTION	f_plane_restr	0.005	2467

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work
1.9-1.9679	0.2692	742	0.2353	13381
1.9679-2.0467	0.2606	691	0.2126	13455
2.0467-2.1398	0.2433	694	0.1883	13420
2.1398-2.2526	0.22	678	0.1727	13493
2.2526-2.3937	0.2201	699	0.1608	13426
2.3937-2.5785	0.2089	741	0.1548	13412
2.5785-2.8378	0.2117	747	0.1612	13439
2.8378-3.2482	0.2196	735	0.1688	13461
3.2482-4.0912	0.1806	680	0.1477	13560
4.0912-33.2637	0.1798	708	0.1565	13628

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	0.8645	0.138	0.2461	0.8863	0.0002	0.3627	0.0368	0.2675	0.0917	-0.2784	-0.0257	0.0894	-0.1101	0.0974	-0.0222	0.1774	-0.0266	0.0177	0.1525	0.0163	0.0591	30.1562	-1.5741	-1.4888
2	0.8566	0.1567	-0.3638	0.4889	-0.0247	0.5802	-0.0158	0.0343	-0.0249	-0.0943	0.0191	0.0103	0.0693	0.1053	-0.0076	0.151	-0.004	-0.0089	0.1215	-0.0322	0.0499	27.0671	-19.2935	4.083
3	0.1286	-0.038	-0.0817	1.642	0.4496	0.9253	-0.0727	-0.2209	0.1324	-0.0762	0.289	-0.4428	-0.0243	0.5287	-0.2006	0.0619	-0.0159	0.0185	0.369	-0.1061	0.1158	50.4574	-12.6504	6.4415
4	0.3574	0.0859	-0.3015	0.2225	0.0723	0.5004	0.099	-0.1788	0.17	0.0588	0.0354	0.0589	-0.1101	0.18	-0.0928	0.1376	-0.068	0.0306	0.1555	-0.0674	0.113	37.0234	2.6907	15.7031
5	0.4515	0.1473	0.0314	0.7746	0.0678	0.5916	-0.018	0.0451	0.2197	-0.0813	0.0408	0.1911	-0.0985	-0.1623	-0.0014	0.1109	0.0036	-0.0447	0.1372	-0.0012	0.179	-2.8812	-15.2196	19.3656
6	0.7383	-0.1911	-0.0441	0.8237	-0.1628	0.6669	0.0909	0.0744	0.1463	-0.0933	0.0278	0.2065	-0.1707	-0.0338	-0.0799	0.136	0.0121	-0.0048	0.0908	-0.0118	0.1664	6.9934	-2.6105	20.0007
7	0.6621	0.3765	-0.1496	0.647	-0.0655	0.737	0.0473	-0.102	0.0222	0.043	-0.0042	0.0632	-0.001	0.0229	-0.0382	0.0992	0.0087	-0.013	0.1038	-0.0204	0.0913	8.3685	-16.8818	30.7989
8	2.9841	0.9561	-1.9327	0.4582	-1.0532	2.5043	-0.3544	0.0277	-0.8814	-0.365	0.0184	-0.0775	0.8499	-0.0065	0.2481	0.2755	-0.0448	-0.0179	0.0808	0.0069	0.2091	3.1328	-37.3889	23.4276
9	0.6064	-0.1313	-0.3614	0.7743	-0.0133	0.6831	-0.1273	-0.4016	0.0192	0.3887	0.0607	-0.1054	0.3001	0.5872	0.0715	0.2582	0.0621	-0.0478	0.3987	0.014	0.0413	36.8685	-26.6062	61.1675
10	0.8823	-0.2668	-0.5834	0.919	0.0415	1.5734	-0.1407	-0.1124	-0.1594	0.1666	-0.019	0.0299	0.3661	0.2443	0.1446	0.2295	0.0709	0.0262	0.1574	0.0153	0.0487	27.9023	-35.2736	49.3033
11	0.3213	0.0091	0.0701	0.1328	-0.1325	0.1447	-0.0648	0.069	0.1021	-0.0126	0.046	0.0475	-0.292	-0.142	0.026	0.3043	0.041	0.0113	0.1676	-0.0141	0.0579	17.9954	-15.049	54.6102
12	0.2398	-0.0474	-0.4181	0.5854	-0.2224	0.8824	0.0052	-0.1491	0.2038	0.2693	0.11	-0.1236	-0.294	0.6772	-0.0785	0.2608	-0.096	-0.0304	0.3664	-0.0565	0.1309	39.5015	-12.1108	53.3975
13	1.038	0.4684	0.3877	0.5736	-0.033	0.2616	0.0158	-0.3531	0.4412	0.0654	-0.2153	0.2811	0.1517	-0.1985	0.1764	0.1503	-0.0337	0.0205	0.2594	-0.1922	0.4597	-7.7172	21.2833	19.6572
14	0.8895	0.4522	0.0955	0.6974	-0.5217	0.7337	0.1335	-0.2699	-0.1015	0.0174	-0.2389	0.2822	0.2758	-0.1864	0.1223	0.1987	-0.0706	0.0111	0.2271	-0.1134	0.392	-11.5057	14.6262	16.9399
15	0.1526	-0.0273	0.132	0.0217	-0.0292	0.1147	0.1395	-0.013	-0.0135	0.086	-0.0841	-0.2857	0.1236	0.1386	-0.067	0.1663	-0.0137	-0.0223	0.0729	-0.0376	0.4322	-10.5476	15.6507	0.3822
16	2.0698	0.1002	0.6822	0.624	-0.0701	0.8453	-0.1855	-0.425	1.196	0.0518	-0.1569	0.1345	-0.1682	-0.1715	0.3426	0.0871	0.0224	-0.0604	0.1143	-0.2987	0.7965	-10.779	33.3411	12.3799
17	0.2881	-0.0756	-0.056	0.5554	0.0864	0.9661	-0.2515	-0.3307	-0.3752	0.1365	0.0268	-0.3642	0.8387	1.0833	0.1137	0.4952	0.5323	0.1138	0.77	0.0562	0.3327	54.4994	-46.2151	30.5238
18	0.3624	-0.1728	-0.5246	0.8113	0.3005	1.1773	-0.0999	-0.3544	-0.016	0.1574	0.1925	-0.4153	0.2665	1.1691	-0.0846	0.1132	0.192	-0.0515	0.7716	-0.0371	0.184	54.768	-30.2125	37.7659
19	0.2608	-0.1872	-0.6162	1.0929	-0.0237	1.6565	0.1749	-0.2496	0.1266	-0.1141	-0.0494	-0.3597	-0.0619	1.0485	-0.0696	0.0404	0.0187	0.0273	0.5728	-0.0343	0.1467	52.7381	-23.165	23.7408
20	0.945	-0.139	-0.5031	1.3351	0.3482	1.2104	-0.2456	0.2236	-0.2712	-0.2827	0.0057	-0.0933	0.7996	0.3872	0.1712	0.4403	0.224	0.0946	0.3275	-0.0695	0.1212	43.8726	-43.3465	18.377
21	0.5709	-0.2565	-0.2268	0.1269	0.2198	0.8543	-0.1587	0.0861	0.7243	-0.1982	-0.2659	0.2957	-0.5501	-0.2391	0.4617	0.4228	0.1741	-0.5567	0.1506	-0.3964	2.4444	75.9124	14.1501	4.2346
22	0.0725	-0.0139	0.0609	0.0093	0.0536	0.626	-0.0752	0.0434	-0.1493	0.3319	-0.2725	-0.2096	-0.4758	-0.0499	0.3382	0.6828	0.009	-0.6539	0.031	-0.1882	2.1896	91.6085	18.373	10.8169
23	0.1703	-0.1243	0.2438	0.3151	-0.385	0.8246	-0.4819	-0.1501	0.8253	0.152	-0.3318	0.165	-0.281	-0.1405	0.7339	0.3628	0.0596	-0.3688	0.1102	-0.3968	1.9819	88.9707	0.9143	15.3887
24	0.2474	-0.2765	-0.0857	0.768	-0.4847	2.797	-0.4149	0.0633	0.7747	-0.1546	-0.2747	0.8532	-0.0704	-0.7995	0.764	0.2497	0.0207	-0.4209	0.2888	-0.3925	2.3168	72.106	-1.54	-1.964

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID -5:72)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 73:214)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 215:241)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 242:294)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID -4:58)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 59:125)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 126:277)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 278:294)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID -2:57)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 58:214)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 215:245)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 246:294)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID -1:52)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 53:76)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 77:93)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 94:294)
17	X-RAY DIFFRACTION	17	(CHAIN E AND RESID -1:61)
18	X-RAY DIFFRACTION	18	(CHAIN E AND RESID 62:146)
19	X-RAY DIFFRACTION	19	(CHAIN E AND RESID 147:204)
20	X-RAY DIFFRACTION	20	(CHAIN E AND RESID 205:294)
21	X-RAY DIFFRACTION	21	(CHAIN F AND RESID 1:77)
22	X-RAY DIFFRACTION	22	(CHAIN F AND RESID 78:96)
23	X-RAY DIFFRACTION	23	(CHAIN F AND RESID 97:208)
24	X-RAY DIFFRACTION	24	(CHAIN F AND RESID 209:294)

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