PDB-7w0i: Crystal structure of threonine aldolase from Mycobacterium vanbaalenii

ID or keywords:

Entry

Database: PDB / ID: 7w0i

Title

Crystal structure of threonine aldolase from Mycobacterium vanbaalenii

Components

L-threonine aldolase

Keywords

TRANSFERASE / Aldolase / threonine / PLP

Function / homology

L-threonine aldolase / threonine aldolase activity / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / amino acid metabolic process / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / L-threonine aldolase

Function and homology information

Biological species

Mycolicibacterium vanbaalenii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Wu, B.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of threonine aldolase from Mycobacterium vanbaalenii
Authors: Wu, B.

History

Deposition	Nov 18, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7w0i_validation.pdf.gz	452.3 KB	Display	wwPDB validaton report
Full document	7w0i_full_validation.pdf.gz	462.9 KB	Display
Data in XML	7w0i_validation.xml.gz	59.4 KB	Display
Data in CIF	7w0i_validation.cif.gz	89.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w0/7w0i ftp://data.pdbj.org/pub/pdb/validation_reports/w0/7w0i	HTTPS FTP

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Related structure data

Related structure data	5vyeS S: Starting model for refinement
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

Deposited unit

A: L-threonine aldolase

B: L-threonine aldolase

C: L-threonine aldolase

D: L-threonine aldolase

146 kDa, 4 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)	96.001, 102.432, 150.352
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 6 - 339 / Label seq-ID: 6 - 339

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B
3	chain C	C	C
4	chain D	D	D

#1: Protein	L-threonine aldolase Mass: 36438.895 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1) (bacteria) Gene: Mvan_1179 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: A1T4B4, low-specificity L-threonine aldolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1288 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

L-threonine aldolase

Mass: 36438.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1) (bacteria)
Gene: Mvan_1179 / Production host:

Escherichia coli K-12 (bacteria)
References: UniProt: A1T4B4, low-specificity L-threonine aldolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1288 / 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: 2.47 Å³/Da / Density % sol: 50.1 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.25M ammonium citrate dibasic, 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.75→48.48 Å / Num. obs: 149478 / % possible obs: 99.82 % / Redundancy: 13 % / CC_1/2: 0.998 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.75→1.813 Å / Num. unique obs: 14780 / CC_1/2: 0.932

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5VYE

5vye

Resolution: 1.75→48.48 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.19	1998	1.34 %
R_work	0.1707	147232	-
obs	0.171	149230	99.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 98.41 Å² / B_iso mean: 28.7257 Å² / B_iso min: 12.59 Å²

Refinement step

Cycle: final / Resolution: 1.75→48.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10016	0	0	1288	11304
B_iso mean	-	-	-	37.98	-
Num. residues	-	-	-	-	1336

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4092	X-RAY DIFFRACTION	2.635	TORSIONAL
1	2	B	4092	X-RAY DIFFRACTION	2.635	TORSIONAL
1	3	C	4092	X-RAY DIFFRACTION	2.635	TORSIONAL
1	4	D	4092	X-RAY DIFFRACTION	2.635	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.75-1.7938	0.2253	156	0.2048	10384	100
1.7938-1.8423	0.2217	119	0.1973	10456	100
1.8423-1.8965	0.2379	157	0.1962	10421	100
1.8965-1.9577	0.2532	138	0.2231	10363	99
1.9577-2.0277	0.2236	129	0.1887	10431	100
2.0277-2.1088	0.2026	153	0.194	10410	100
2.1088-2.2048	0.2368	139	0.1784	10489	100
2.2048-2.3211	0.2264	141	0.1872	10409	99
2.3211-2.4665	0.2123	145	0.1733	10513	100
2.4665-2.6569	0.1883	137	0.1709	10494	100
2.6569-2.9243	0.2003	146	0.1818	10575	100
2.9243-3.3473	0.1948	147	0.1661	10584	100
3.3473-4.2169	0.1516	145	0.1444	10680	100
4.2169-48.336	0.1538	146	0.1568	11023	100

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	0.4315	-0.1635	0.1091	0.6604	0.1236	2.3826	-0	0.0332	-0.0724	-0.0762	0.0759	-0.1418	0.0877	0.3229	-0.0246	0.191	0.0025	0.0286	0.1789	-0.0149	0.2418	2.6472	-18.3907	36.1812
2	0.7217	0.1156	0.4052	0.509	0.0197	0.9027	-0.0228	0.0097	0.0463	0.0438	0.0066	-0.0452	-0.0701	0.109	0.0204	0.167	-0.0219	-0.0011	0.159	-0.0101	0.1911	-2.7271	0.8499	34.9014
3	1.1028	-0.3858	-0.6188	0.4899	0.5106	0.682	0.0224	0.1541	0.0847	-0.1764	-0.0162	-0.0367	-0.1247	-0.0554	0.0057	0.21	-0.0014	-0.0137	0.1687	0.0171	0.1726	-12.1661	6.5328	21.5769
4	0.3879	-0.2576	0.1577	1.4796	0.7374	0.6085	-0.0207	0.1105	0.0361	-0.0905	0.0107	-0.0454	-0.0727	0.086	0.0069	0.1747	-0.0363	0.0213	0.1877	0.0048	0.1879	1.335	1.7216	24.3245
5	0.1977	-0.1553	-0.0835	0.4638	0.017	0.8696	-0.0226	0.0278	-0.0343	-0.0592	0.0077	-0.0674	0.0411	0.1642	0.0055	0.1652	-0.0126	0.0156	0.1723	-0.0065	0.2026	1.2619	-7.7643	30.4695
6	1.1893	0.0003	-0.2181	1.8146	-0.3754	1.8898	0.0287	0.1304	-0.0211	-0.3941	-0.0971	0.3957	0.2001	-0.3137	0.0347	0.3217	-0.0061	-0.0232	0.2821	-0.0495	0.2387	-8.5431	-15.2901	5.8613
7	0.8616	0.1103	0.1014	0.5777	-0.1534	1.7736	-0.0041	0.0697	-0.0664	-0.0689	0.0009	0.0482	0.1906	-0.1968	-0.0327	0.3094	-0.0188	0.0281	0.2566	-0.0441	0.2265	-5.5513	-19.3228	11.1385
8	0.4915	-0.3739	0.3431	0.8105	-0.1936	2.2961	0.0641	0.0516	-0.1288	-0.1325	-0.0161	-0.0121	0.134	0.092	-0.0162	0.1458	-0.0012	0.0215	0.136	-0.0089	0.1955	-3.1087	-24.1192	40.1845
9	0.8059	0.18	0.1724	0.3744	0.1847	1.3951	-0.0242	0.0149	-0.1004	-0.0705	0.0035	0.0121	0.1193	-0.104	0.0052	0.1761	-0.0258	0.0053	0.1557	0.0017	0.1993	-22.1359	-18.2372	42.0399
10	0.7889	-0.1954	0.3509	1.1185	-0.3907	0.5307	-0.076	-0.2068	-0.0033	0.1438	0.0824	0.076	-0.0816	-0.2351	-0.0089	0.1511	0.0309	0.0288	0.225	-0.0059	0.1603	-27.3219	-9.0097	55.7989
11	1.3513	-0.3328	0.7404	0.7323	0.1547	0.3838	-0.0177	-0.0836	-0.0852	0.0446	0.029	0.0461	0.113	-0.1303	-0.0211	0.1638	-0.0155	0.0066	0.1877	0.0229	0.2094	-22.8983	-22.5367	52.5054
12	0.7705	0.5328	-0.4044	0.6581	-0.349	0.9972	0.0478	-0.0676	-0.0678	-0.0335	0.0324	0.0282	0.0328	-0.0466	-0.0659	0.1528	-0.0012	-0.0025	0.1421	0.0032	0.1796	-21.5467	-15.8895	36.6965
13	0.4895	0.0035	0.4868	0.9872	-0.505	0.9558	0.0458	-0.0259	-0.0973	0.021	0.0019	-0.0191	0.304	-0.0301	-0.0476	0.1823	0.03	0.0003	0.1538	0.004	0.2083	-7.3897	-27.4162	53.3047
14	1.8838	-0.6622	-0.6909	1.6596	-0.0415	2.7508	-0.0098	-0.3453	0.6147	0.3521	0.0785	-0.2037	-0.4942	0.2966	-0.1389	0.3152	-0.0135	-0.0394	0.2793	-0.0599	0.2984	-5.2843	-13.6286	70.7681
15	1.7358	-0.1843	-0.1461	2.1655	0.258	2.2092	-0.0213	-0.2878	0.1843	0.2175	0.0216	-0.1853	-0.2576	0.1636	-0.0136	0.2598	-0.0102	-0.0276	0.2326	0.0025	0.2034	-1.2965	-16.2318	65.4861
16	0.8474	-0.3005	-0.1715	0.8378	-0.6313	1.8736	-0.101	-0.2082	0.1927	0.21	0.1425	0.1093	-0.2605	-0.258	-0.018	0.2624	0.1068	-0.0391	0.3227	-0.0417	0.2635	-48.6415	24.5574	35.7524
17	0.9401	-0.2391	0.0338	0.4341	-0.2616	1.1353	-0.037	-0.026	-0.0325	0.009	0.0017	0.1737	-0.024	-0.2513	0.0369	0.1697	0.0165	-0.013	0.2412	-0.0269	0.2503	-42.197	6.464	30.0817
18	1.1111	-0.7042	0.2904	0.7877	-0.2637	0.7539	0.0564	0.2006	0.0024	-0.1822	-0.1022	0.02	-0.0166	-0.0543	0.0401	0.2019	0.0169	-0.0042	0.1999	-0.0105	0.1749	-29.1227	4.8332	18.7936
19	0.8919	-0.3973	-0.189	1.1861	-0.357	0.2376	0.0223	0.1261	-0.0121	-0.1598	-0.0075	0.1179	-0.0434	-0.1326	0.0043	0.2086	0.0314	-0.0467	0.2663	-0.0281	0.2325	-43.0489	9.1654	19.076
20	0.7229	0.1296	0.4946	0.4204	0.0549	1.2166	-0.0452	-0.0683	0.0431	-0.0331	0.0388	0.0565	-0.0039	-0.1459	0.0047	0.1619	0.0348	-0.0159	0.2119	-0.0141	0.2075	-41.6151	5.257	35.776
21	1.0494	-0.2698	0.3583	1.0008	-0.6849	0.9178	-0.0481	0.0524	0.1488	-0.0496	0.0134	0.1084	-0.0422	-0.1172	0.0779	0.2119	0.081	-0.0335	0.2628	-0.0199	0.2787	-47.6795	24.4578	21.5107
22	1.9321	-1.0686	-0.7328	1.2637	0.1757	3.2227	0.1857	0.0632	0.3775	0.0397	-0.1389	-0.6566	-0.4037	0.6997	-0.0978	0.3179	-0.0135	-0.0319	0.4337	0.0708	0.4479	-29.093	30.5998	10.5857
23	3.1995	-0.2606	-0.4374	1.9311	-0.0455	2.4072	0.1459	-0.02	0.4167	-0.0683	-0.1673	-0.3028	-0.2813	0.5318	0.0692	0.312	0.0223	-0.0389	0.3508	0.0488	0.3667	-33.5007	33.0482	15.8035
24	1.0621	0.1828	-0.4734	0.8092	-0.6405	2.0908	-0.0458	-0.133	0.2927	0.191	0.0528	0.0512	-0.4345	-0.3088	0.0103	0.3382	0.1642	-0.0391	0.3688	-0.0774	0.3223	-44.4878	28.4095	43.0327
25	0.5859	-0.1461	0.0867	0.6325	-0.5134	0.7871	-0.1955	-0.1063	0.2692	0.2478	0.0365	-0.1327	-0.3923	-0.1584	0.1255	0.3141	0.0838	-0.0801	0.188	-0.0676	0.2615	-26.5522	21.2262	48.1674
26	1.0438	-0.4035	0.2611	0.8834	0.2437	1.1256	-0.1977	-0.3399	0.1416	0.2138	0.0901	-0.0033	-0.1587	-0.2086	0.0955	0.2295	0.0795	-0.0203	0.2242	-0.0362	0.1658	-25.0394	7.8401	59.044
27	1.0318	-0.1857	-0.6025	0.9464	-0.1848	0.4043	-0.2598	-0.2329	0.2807	0.2805	0.0478	-0.0655	-0.3574	-0.2498	0.0687	0.3837	0.1579	-0.0802	0.2908	-0.1342	0.2609	-28.9594	21.9315	59.2417
28	0.4838	0.4369	0.6088	0.4909	0.0959	1.4976	-0.112	-0.1454	0.1299	0.127	-0.0051	-0.0288	-0.1166	-0.0849	0.1171	0.2542	0.0546	-0.0552	0.1954	-0.0489	0.2603	-25.506	20.7587	42.4135
29	0.4819	0.2972	-0.2599	0.0539	0.0693	0.9098	0.0416	-0.0912	0.2204	0.2645	0.0016	0.0287	-0.6733	-0.4031	-0.0938	0.4138	0.2238	-0.0326	0.4094	-0.0926	0.3306	-44.0739	27.1081	57.3018
30	1.5	-0.3006	0.8728	1.3521	-0.4578	2.4651	-0.1278	-0.1781	-0.3781	-0.0459	-0.0103	-0.0139	0.5003	-0.4647	0.0765	0.4425	0.1284	0.068	0.6202	-0.0882	0.3145	-50.6601	8.3861	67.9956
31	0.6275	0.3961	-0.2559	1.6283	-0.4263	1.5701	-0.0146	0.0939	-0.07	-0.1134	-0.0789	0.1853	0.2452	-0.5222	0.0917	0.3863	0.139	0.0143	0.6171	-0.0998	0.28	-53.0383	13.0166	62.8651

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 39 )	A	6 - 39
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 87 )	A	40 - 87
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 154 )	A	88 - 154
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 155 through 212 )	A	155 - 212
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 213 through 276 )	A	213 - 276
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 277 through 304 )	A	277 - 304
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 305 through 339 )	A	305 - 339
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 6 through 39 )	B	6 - 39
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 87 )	B	40 - 87
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 88 through 154 )	B	88 - 154
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 155 through 212 )	B	155 - 212
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 213 through 239 )	B	213 - 239
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 240 through 276 )	B	240 - 276
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 277 through 304 )	B	277 - 304
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 305 through 339 )	B	305 - 339
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 6 through 39 )	C	6 - 39
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 40 through 87 )	C	40 - 87
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 88 through 154 )	C	88 - 154
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 155 through 212 )	C	155 - 212
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 213 through 239 )	C	213 - 239
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 240 through 276 )	C	240 - 276
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 277 through 304 )	C	277 - 304
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 305 through 339 )	C	305 - 339
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 6 through 39 )	D	6 - 39
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 40 through 87 )	D	40 - 87
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 88 through 154 )	D	88 - 154
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 155 through 212 )	D	155 - 212
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 213 through 239 )	D	213 - 239
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 240 through 276 )	D	240 - 276
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 277 through 304 )	D	277 - 304
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 305 through 339 )	D	305 - 339

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