PDB-6nst: Crystal structure of branched chain amino acid aminotransferase f...

ID or keywords:

Entry

Database: PDB / ID: 6nst

Title

Crystal structure of branched chain amino acid aminotransferase from Pseudomonas aeruginosa

Components

Branched-chain-amino-acid aminotransferase

Keywords

TRANSFERASE / CSGID / aminostransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

: / L-aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-valine-2-oxoglutarate transaminase activity / L-isoleucine-2-oxoglutarate transaminase activity / L-leucine-2-oxoglutarate transaminase activity / branched-chain-amino-acid transaminase / L-leucine biosynthetic process / L-valine biosynthetic process / isoleucine biosynthetic process / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.136 Å

Authors

Chang, C. / Skarina, T. / Savshenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of branched chain amino acid aminotransferase from Pseudomonas aeruginosa
Authors: Chang, C. / Skarina, T. / Savshenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 25, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6nst.cif.gz	699.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6nst.ent.gz	579.2 KB	Display	PDB format
PDBx/mmJSON format	6nst.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/ns/6nst ftp://data.pdbj.org/pub/pdb/validation_reports/ns/6nst	HTTPS FTP

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Related structure data

Related structure data	3u0gS S: Starting model for refinement
Similar structure data	3u0g-d 4whx-d 5cm0-1 2ej0-d 1a3g-1 2ej2-d 5ce8-1 2eiy-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95866

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (5)

Deposited unit

A: Branched-chain-amino-acid aminotransferase

B: Branched-chain-amino-acid aminotransferase

C: Branched-chain-amino-acid aminotransferase

D: Branched-chain-amino-acid aminotransferase

E: Branched-chain-amino-acid aminotransferase

F: Branched-chain-amino-acid aminotransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	85.837, 129.636, 85.787
Angle α, β, γ (deg.)	90.000, 114.250, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Branched-chain-amino-acid aminotransferase / BCAT Mass: 34151.598 Da / Num. of mol.: 6 / Mutation: L31H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ilvE, PA5013 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O86428, branched-chain-amino-acid transaminase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.14 Å³/Da / Density % sol: 42.43 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG3350 25%, ammonium acetate 0.2M, Bis-Tris 0.1 M

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97929 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 28, 2018

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97929 Å / Relative weight: 1

Reflection

Resolution: 2.15→50 Å / Num. obs: 83927 / % possible obs: 91.4 % / Redundancy: 4.1 % / R_merge(I) obs: 0.121 / R_pim(I) all: 0.059 / R_rim(I) all: 0.135 / Χ²: 0.925 / Net I/σ(I): 8.8 / Num. measured all: 342339

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.15-2.19	2.1	0.419	3010	0.696	0.323	0.532	1.072	65.6
2.19-2.23	2.1	0.389	3046	0.734	0.305	0.498	1.064	66.9
2.23-2.27	2.1	0.365	3046	0.76	0.282	0.464	1.181	67
2.27-2.32	2.2	0.311	3044	0.83	0.238	0.394	1.137	66.2
2.32-2.37	2.8	0.285	3765	0.901	0.184	0.342	1.092	82.2
2.37-2.42	3.5	0.297	4443	0.899	0.175	0.347	1.144	96.8
2.42-2.48	3.6	0.286	4446	0.894	0.167	0.333	1.097	97.6
2.48-2.55	3.7	0.267	4496	0.917	0.155	0.311	1.073	98.2
2.55-2.62	3.8	0.245	4502	0.921	0.141	0.284	1.049	98.3
2.62-2.71	3.9	0.24	4484	0.923	0.136	0.278	1.054	98.1
2.71-2.81	4	0.225	4461	0.933	0.126	0.259	1.066	97.1
2.81-2.92	4.4	0.21	4553	0.949	0.111	0.239	0.987	99.2
2.92-3.05	4.6	0.196	4540	0.964	0.101	0.221	0.974	99.1
3.05-3.21	4.8	0.182	4543	0.972	0.091	0.204	0.956	99.4
3.21-3.41	4.8	0.156	4534	0.974	0.077	0.174	0.947	98.4
3.41-3.68	5.1	0.143	4592	0.978	0.069	0.16	0.893	99.5
3.68-4.05	5.3	0.127	4578	0.984	0.059	0.14	0.786	99.7
4.05-4.63	5.3	0.106	4562	0.987	0.05	0.118	0.73	99
4.63-5.83	5.4	0.099	4612	0.99	0.045	0.109	0.63	99.8
5.83-50	5.3	0.094	4670	0.985	0.045	0.105	0.701	99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.24	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3u0g

3u0g

Resolution: 2.136→49.919 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2526	3816	4.83 %
R_work	0.1946	75165	-
obs	0.1974	78981	83.43 %

Solvent computation

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

Displacement parameters

B_iso max: 130.14 Å² / B_iso mean: 30.742 Å² / B_iso min: 4.15 Å²

Refinement step

Cycle: final / Resolution: 2.136→49.919 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13922	0	30	487	14439
B_iso mean	-	-	37.95	25.69	-
Num. residues	-	-	-	-	1794

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.136-2.163	0.5793	5	0.2499	217	222	6
2.163-2.1914	0.3016	47	0.2652	988	1035	29
2.1914-2.2215	0.3181	74	0.2593	1350	1424	41
2.2215-2.2532	0.3259	96	0.2545	1549	1645	47
2.2532-2.2868	0.3019	100	0.2509	1601	1701	49
2.2868-2.3226	0.3425	94	0.2439	1883	1977	56
2.3226-2.3606	0.3138	115	0.2457	2112	2227	64
2.3606-2.4014	0.29	163	0.2265	3075	3238	92
2.4014-2.445	0.3414	154	0.2244	3206	3360	95
2.445-2.492	0.2901	139	0.2328	3211	3350	97
2.492-2.5429	0.297	196	0.2286	3217	3413	97
2.5429-2.5982	0.2773	146	0.2247	3272	3418	98
2.5982-2.6586	0.2984	148	0.2328	3272	3420	98
2.6586-2.7251	0.3261	184	0.2259	3220	3404	98
2.7251-2.7988	0.3052	185	0.221	3166	3351	95
2.7988-2.8811	0.281	148	0.222	3314	3462	99
2.8811-2.9741	0.2989	186	0.2201	3279	3465	99
2.9741-3.0804	0.2982	172	0.2214	3307	3479	99
3.0804-3.2037	0.257	142	0.2089	3341	3483	99
3.2037-3.3495	0.2341	151	0.2004	3298	3449	99
3.3495-3.526	0.2507	177	0.184	3278	3455	98
3.526-3.7469	0.2209	153	0.1762	3345	3498	99
3.7469-4.0361	0.2087	147	0.1591	3335	3482	100
4.0361-4.442	0.1976	164	0.1457	3336	3500	99
4.442-5.0843	0.1945	180	0.1436	3291	3471	99
5.0843-6.4035	0.2123	186	0.1775	3335	3521	100
6.4035-49.933	0.2	164	0.1742	3367	3531	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	0.8795	-0.1789	0.2654	1.1884	0.2288	0.869	-0.0297	0.1276	0.0847	-0.0724	0.1157	0.177	-0.0947	-0.3018	-0.0287	0.1322	0.0015	0.0171	0.229	0.11	0.1963	7.9136	26.1428	-1.4451
2	0.5941	0.3607	0.1127	0.3259	-0.2182	1.3735	0.0835	0.0816	0.3534	-0.0433	0.037	0.1268	-0.2337	-0.1454	-0.028	0.0978	0.0235	0.0039	0.1321	0.0212	0.1881	8.3322	13.0975	17.5056
3	0.3314	0.0514	0.1475	1.1534	-0.6927	0.9819	0.0309	0.0905	0.1529	0.0568	-0.0031	-0.0081	-0.3006	-0.061	0.0047	0.1923	0.0378	0.0528	0.1236	0.0083	0.1904	11.4582	26.1511	25.6115
4	0.4717	0.2043	-0.0418	0.3785	0.2733	1.0659	-0.041	0.4055	0.1751	-0.3708	0.1847	0.2056	-0.1976	-0.2542	0.4036	0.2311	-0.1633	-0.1258	0.4825	0.0745	0.1494	0.1406	2.0853	-8.7667
5	0.6396	-0.4759	0.4132	0.3631	-0.2575	0.5492	0.1476	0.3395	0.0945	-0.3322	-0.054	-0.0311	0.0512	0.0229	-0.0598	0.5323	-0.0993	-0.004	0.5385	0.0225	0.1472	12.3595	-0.9062	-15.0736
6	0.6188	-0.1144	-0.2447	0.0689	0.0247	0.1179	-0.0937	0.0966	0.0356	-0.1057	0.1047	0.098	0.1026	-0.2385	-0.011	0.1218	-0.0289	0.0006	0.1313	0.0348	0.1087	21.6469	1.212	1.537
7	0.8426	0.2552	0.5528	0.2792	0.1183	0.3922	-0.131	0.2247	-0.1333	-0.1956	0.0744	0.0081	0.2949	-0.2265	-0.0694	0.3	-0.135	0.0211	0.2755	-0.0884	0.1373	21.5519	-14.5906	-6.4372
8	0.8235	0.6096	0.1773	0.8151	0.2493	0.8785	0.1415	-0.2268	0.0625	0.1955	-0.1139	0.1055	-0.0432	0.0224	-0.0075	0.2416	-0.0328	0.0302	0.1539	-0.0285	0.1187	13.1695	4.743	55.0654
9	0.3823	-0.219	-0.3914	0.2006	0.0831	0.5426	0.0317	-0.0545	-0.0406	0.1407	-0.0411	0.0316	0.0316	0.0026	-0.0047	0.2316	-0.0051	-0.0181	0.1556	0.0064	0.1121	22.4836	-0.7878	43.7985
10	0.6752	-0.6216	-0.8745	0.6882	0.9481	1.3506	0.0871	-0.031	0.069	0.1267	0.0067	-0.0168	-0.2139	0.171	-0.0198	0.2412	-0.0132	-0.0022	0.1973	-0.0568	0.1481	35.8056	13.1088	43.8675
11	0.5767	0.3273	0.1463	0.6466	0.1819	0.8211	0.0314	-0.1924	-0.0689	0.2321	-0.0589	0.03	0.1181	-0.0764	0.0094	0.2734	0.0043	0.0096	0.1174	0.0187	0.0786	8.5657	-22.4201	45.4149
12	0.1359	-0.0658	-0.1557	0.7343	-0.516	0.6658	-0.0121	-0.0943	-0.0083	0.198	-0.0038	0.0807	0.0293	-0.0248	0.0201	0.1456	-0.0057	0.0108	0.1384	-0.0121	0.0953	8.3616	-10.9358	34.9689
13	0.1925	0.0909	-0.1332	1.2565	-0.7164	0.882	-0.1598	0.123	-0.1258	-0.1231	0.1182	-0.0405	0.3672	-0.1071	0.0135	0.1692	-0.0792	-0.0049	0.1458	-0.0058	0.1317	2.0626	-19.9652	19.7029
14	0.7981	0.2283	-0.038	0.4726	-0.1313	0.9173	0.0645	-0.0725	0.204	-0.0197	0.0439	-0.4513	0.2021	0.2657	0.1253	-0.039	-0.0208	0.0405	0.2507	-0.0731	0.4038	60.9528	5.6776	17.8996
15	0.0955	-0.1799	0.1328	0.3251	-0.2478	0.3778	-0.0562	-0.0575	-0.0802	0.0345	0.0312	-0.2048	-0.0307	0.1425	0.0341	0.0396	-0.0076	0.0153	0.1335	-0.0138	0.127	39.2153	5.8809	10.8255
16	1.5486	0.2453	0.5663	0.2888	0.1418	0.498	0.0435	-0.0381	0.2684	-0.0676	0.0749	-0.1817	-0.2725	0.1266	0.0583	0.0918	-0.0743	0.0163	0.1352	-0.0819	0.2455	41.829	23.2043	13.288
17	1.7234	-0.267	-0.3407	2.2864	0.2885	0.1413	-0.0238	-0.299	0.0067	0.0739	-0.0132	-0.6078	0.022	0.1942	0.0097	0.1333	-0.0018	0.0342	0.2076	0.0125	0.3724	60.8698	-13.1135	10.6678
18	0.9188	-0.1876	0.1093	1.0051	0.2616	0.5996	0.0163	0.0381	-0.099	-0.0627	-0.02	-0.2089	0.1258	0.1055	-0.0041	0.1569	0.0279	0.0505	0.1097	-0.0095	0.1895	51.7528	-20.4816	7.2863
19	0.0912	0.1448	-0.2104	0.2758	-0.2835	0.5113	-0.0311	-0.0889	-0.0389	-0.038	0.0085	-0.2006	0.03	0.1263	0.017	0.0959	0.0354	-0.0134	0.1688	-0.0017	0.1555	38.3494	-11.4726	22.9276
20	0.817	-0.1503	-0.4475	0.5675	0.4804	0.9124	-0.1125	-0.0262	-0.1179	-0.0048	0.0505	-0.1133	0.1881	0.0436	0.026	0.1498	0.0409	0.0317	0.0715	0.0044	0.1058	34.0589	-28.5774	20.6946

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 1 through 126 )	A	1 - 126
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 127 through 198 )	A	127 - 198
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 199 through 307 )	A	199 - 307
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 117 )	B	2 - 117
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 118 through 139 )	B	118 - 139
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 140 through 198 )	B	140 - 198
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 199 through 306 )	B	199 - 306
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 89 )	C	1 - 89
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 90 through 198 )	C	90 - 198
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 199 through 307 )	C	199 - 307
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 89 )	D	2 - 89
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 90 through 198 )	D	90 - 198
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 199 through 307 )	D	199 - 307
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 1 through 139 )	E	1 - 139
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 140 through 198 )	E	140 - 198
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 199 through 307 )	E	199 - 307
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 1 through 40 )	F	1 - 40
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 41 through 139 )	F	41 - 139
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 140 through 198 )	F	140 - 198
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 199 through 307 )	F	199 - 307

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