PDB-6f35: Crystal structure of the aspartate aminotranferase from Rhizobium...

ID or keywords:

Entry

Database: PDB / ID: 6f35

Title

Crystal structure of the aspartate aminotranferase from Rhizobium meliloti

Components

Aspartate aminotransferase B

Keywords

TRANSFERASE / Aspartate Amino-transferase

Function / homology

Function and homology information

2-aminoadipate transaminase / 2-aminoadipate transaminase activity / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function

Biological species

Rhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Cobessi, D. / Graindorge, M. / Giustini, C. / Matringe, M.

Citation

Journal: Febs J. / Year: 2019
Title: Tyrosine metabolism: identification of a key residue in the acquisition of prephenate aminotransferase activity by 1 beta aspartate aminotransferase.
Authors: Giustini, C. / Graindorge, M. / Cobessi, D. / Crouzy, S. / Robin, A. / Curien, G. / Matringe, M.

History

Deposition	Nov 28, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 12, 2019	Group: Data collection / Database references Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2	Jan 17, 2024	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	6f35.cif.gz	338.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6f35.ent.gz	276.4 KB	Display	PDB format
PDBx/mmJSON format	6f35.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/f3/6f35 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f35	HTTPS FTP

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Related structure data

Related structure data	6f5vC 6f77C 1j32S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6f77-3 2fni-d 5zsp-d 2ay6-d 4rkd-1 2hp0-d 1p3w-d 6l1o-d 3asa-1 3tat-2 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: Aspartate aminotransferase B

B: Aspartate aminotransferase B

hetero molecules

89.8 kDa, 2 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)	72.200, 117.280, 127.300
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Aspartate aminotransferase B / AspAT / Transaminase A Mass: 44453.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Pyridoxal phosphate bound to Lys (LLP) Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria) Strain: 1021 / Gene: aatB, R03291, SMc04386 / Production host: Escherichia coli (E. coli) / References: UniProt: P58350, aspartate transaminase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 851 / 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: 3.02 Å³/Da / Density % sol: 59.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 4.5 Details: 0.1 M Na acetate pH 4.5, 5% PEG 4K. The protein concentrations ranged from 5 mg/ml to 10 mg/ml.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2010 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9797 Å / Relative weight: 1
Reflection	Resolution: 1.9→47.75 Å / Num. obs: 85690 / % possible obs: 99.8 % / Redundancy: 6.43 % / R_sym value: 0.107 / Net I/σ(I): 14.64
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 6.33 % / Mean I/σ(I) obs: 3.27 / Num. unique obs: 6128 / R_sym value: 0.609 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1J32

1j32

Resolution: 1.9→47.746 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1807	4283	5 %
R_work	0.1525	-	-
obs	0.1539	85621	99.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→47.746 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6071	0	58	851	6980

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6435
X-RAY DIFFRACTION	f_angle_d	0.859	8781
X-RAY DIFFRACTION	f_dihedral_angle_d	10.156	3931
X-RAY DIFFRACTION	f_chiral_restr	0.052	985
X-RAY DIFFRACTION	f_plane_restr	0.005	1146

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 (%)
1.9-1.9216	0.2583	149	0.2196	2535	X-RAY DIFFRACTION	96
1.9216-1.9442	0.2919	160	0.2086	2658	X-RAY DIFFRACTION	100
1.9442-1.968	0.2322	139	0.2018	2668	X-RAY DIFFRACTION	100
1.968-1.9929	0.2362	112	0.1918	2731	X-RAY DIFFRACTION	100
1.9929-2.0191	0.2103	148	0.1784	2680	X-RAY DIFFRACTION	100
2.0191-2.0468	0.2476	126	0.1658	2685	X-RAY DIFFRACTION	100
2.0468-2.076	0.2093	151	0.168	2659	X-RAY DIFFRACTION	100
2.076-2.107	0.1901	156	0.1589	2692	X-RAY DIFFRACTION	100
2.107-2.1399	0.1921	154	0.1633	2666	X-RAY DIFFRACTION	100
2.1399-2.175	0.178	145	0.152	2699	X-RAY DIFFRACTION	100
2.175-2.2125	0.2002	144	0.1557	2691	X-RAY DIFFRACTION	100
2.2125-2.2527	0.1994	147	0.1545	2706	X-RAY DIFFRACTION	100
2.2527-2.296	0.1861	155	0.1564	2658	X-RAY DIFFRACTION	100
2.296-2.3429	0.168	128	0.1545	2722	X-RAY DIFFRACTION	100
2.3429-2.3939	0.2139	142	0.1534	2685	X-RAY DIFFRACTION	100
2.3939-2.4495	0.2076	130	0.1509	2712	X-RAY DIFFRACTION	100
2.4495-2.5108	0.1962	139	0.1545	2708	X-RAY DIFFRACTION	100
2.5108-2.5787	0.1861	148	0.1484	2702	X-RAY DIFFRACTION	100
2.5787-2.6546	0.2042	147	0.1538	2711	X-RAY DIFFRACTION	100
2.6546-2.7402	0.1844	154	0.157	2677	X-RAY DIFFRACTION	100
2.7402-2.8382	0.1994	123	0.1518	2742	X-RAY DIFFRACTION	100
2.8382-2.9518	0.172	136	0.1512	2717	X-RAY DIFFRACTION	100
2.9518-3.0861	0.1692	160	0.1424	2713	X-RAY DIFFRACTION	100
3.0861-3.2488	0.154	129	0.1499	2749	X-RAY DIFFRACTION	100
3.2488-3.4522	0.1587	143	0.1529	2746	X-RAY DIFFRACTION	100
3.4522-3.7187	0.1695	126	0.1412	2742	X-RAY DIFFRACTION	100
3.7187-4.0927	0.1637	140	0.1341	2775	X-RAY DIFFRACTION	100
4.0927-4.6845	0.1308	148	0.1179	2780	X-RAY DIFFRACTION	100
4.6845-5.9003	0.1475	150	0.1406	2802	X-RAY DIFFRACTION	100
5.9003-47.7606	0.1613	154	0.1623	2927	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	1.027	-0.6642	-0.04	2.562	-3.4094	5.2636	0.0667	-0.3773	-0.0108	0.2032	0.035	-0.0337	-0.1008	-0.1093	-0.1025	0.1786	-0.0644	-0.0478	0.2144	-0.0214	0.137	4.2612	41.143	-12.9124
2	0.831	0.2907	-0.199	0.4804	0.3314	1.4212	0.0306	-0.1644	-0.1442	0.0842	-0.0892	-0.1524	0.2989	0.1504	0.0268	0.1859	0.0004	-0.0158	0.181	0.0907	0.2165	-3.1328	22.761	-9.0769
3	1.9495	-0.1232	-0.7841	0.7355	-0.271	0.9982	-0.1404	0.292	-0.5235	-0.0563	0.0541	0.0092	0.3495	-0.0918	0.0516	0.2199	-0.018	-0.0101	0.1075	-0.0449	0.2017	-6.6748	18.7426	-37.6392
4	3.8664	1.4637	0.1524	2.8876	0.2679	1.709	-0.0312	0.2074	-0.0283	-0.1531	0.0359	0.1596	0.0351	-0.0763	-0.0073	0.082	0.006	-0.005	0.0751	0.0117	0.0715	-10.3236	34.0632	-35.8889
5	4.7293	0.3016	-2.6984	0.0928	-0.2069	5.0555	0.0168	-0.1589	0.0462	0.0577	0.0422	-0.0119	-0.0665	0.0888	-0.0604	0.0876	-0.0033	0.0021	0.0625	-0.0123	0.1213	-10.1781	46.2631	-23.0826
6	0.902	0.4216	-0.1267	3.4876	-2.4982	2.8704	0.0091	-0.2001	0.0377	0.1803	0.0808	0.1766	-0.1373	-0.2303	-0.0999	0.0793	0.0067	0.0075	0.1481	0.0119	0.1355	-21.7027	42.4286	-20.6264
7	1.859	-0.0289	-0.359	0.5275	-0.1174	0.9633	-0.035	0.0226	-0.0964	-0.0524	0.0448	0.1	0.1297	-0.1608	-0.0124	0.1095	-0.0223	-0.0146	0.0837	0.0015	0.1021	-15.5515	31.5719	-31.2241
8	2.88	-1.2897	-2.372	2.1365	2.1256	6.4645	-0.0823	-0.2581	-0.3041	0.3142	0.0257	0.0277	0.4477	-0.1866	0.1063	0.1511	-0.0581	-0.0117	0.2268	0.1074	0.1889	-19.1279	22.9145	-8.5454
9	3.3025	-0.1298	1.7116	3.2573	0.5954	5.5365	-0.0711	-0.7057	0.2268	0.6151	-0.0566	-0.2243	-0.3334	0.1162	0.0845	0.2654	-0.043	-0.0424	0.3304	0.0044	0.1487	-10.5613	38.4109	4.5042
10	1.3355	0.1257	0.4639	1.0953	-0.3303	1.6162	-0.0353	-0.2597	-0.0803	0.268	-0.0289	-0.1648	-0.096	-0.013	0.0668	0.1261	-0.0073	-0.0224	0.1901	0.0375	0.1282	-11.0236	33.6806	-5.6089
11	2.4796	-2.4435	-1.2153	9.0362	3.0909	2.834	-0.0877	-0.6308	-0.152	0.9257	0.2244	-0.1755	0.6153	0.1327	-0.1063	0.2818	-0.0622	-0.0763	0.4395	0.1765	0.2395	-11.0934	25.1717	5.3303
12	0.4243	0.5914	0.0968	1.7292	2.3987	4.1543	-0.0546	0.1769	0.0037	-0.1579	0.132	0.1194	-0.2441	0.1247	-0.0607	0.1173	0.0218	-0.0257	0.1604	0.0268	0.1558	-2.1874	39.0911	-51.5279
13	0.7167	-0.1794	-0.3358	0.4612	-0.0948	1.6142	-0.0793	-0.0476	-0.2677	0.0128	0.0795	0.011	0.4699	0.1008	-0.0069	0.1885	0.0207	0.0026	0.1079	0.0067	0.2221	7.5922	19.3948	-36.7898
14	1.7635	-0.2164	-0.543	1.3685	-0.2813	1.5499	-0.0144	-0.0948	0.0043	0.0491	0.0603	-0.0782	0.025	0.1351	-0.0461	0.0698	0.006	-0.0094	0.0881	-0.0176	0.078	14.3205	39.1828	-33.6135
15	1.7577	-1.2814	-0.3367	2.6984	0.7287	1.3992	0.0528	0.126	0.1142	-0.1667	-0.0479	-0.3877	-0.0808	0.2104	-0.013	0.0905	0.0016	0.0209	0.1604	0.0255	0.1644	24.6383	46.4505	-40.6993
16	0.7838	-0.022	0.0414	0.9759	0.3487	0.6908	-0.0177	0.0696	-0.0515	0.0655	0.0789	-0.1729	0.1204	0.2083	-0.0659	0.1039	0.0401	-0.0067	0.1405	0.0054	0.1077	20.9548	32.1717	-35.4959
17	2.5	-1.5363	-1.0084	5.0381	0.1389	0.7701	-0.0678	-0.1999	-0.1399	0.2084	0.0555	-0.0351	0.1626	0.1683	-0.0056	0.1446	0.0449	-0.0214	0.1443	0.0347	0.0447	10.3919	30.2727	-25.7777
18	1.9591	0.8876	-1.9064	2.8811	-2.3087	5.9794	-0.093	-0.029	-0.137	-0.142	0.0036	-0.1652	0.4679	0.338	0.1386	0.1039	0.0443	0.0115	0.1632	-0.0544	0.1587	24.3497	24.8888	-54.3757
19	1.894	0.1587	-0.1529	2.1681	-0.1249	2.1147	-0.0428	0.2298	0.1088	-0.1169	-0.0605	0.1361	-0.067	-0.1829	0.0999	0.1009	0.018	-0.0019	0.1433	-0.0372	0.1181	13.0927	36.1461	-64.4523
20	1.9448	1.4606	-1.381	5.8864	-6.7007	7.5673	0.0187	0.395	-0.2485	-0.4898	0.0465	-0.0053	0.5814	-0.0007	-0.0608	0.2551	0.0277	-0.0067	0.2108	-0.0973	0.1831	15.0775	25.0552	-68.8227

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 56 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 95 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 96 through 121 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 122 through 153 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 154 through 192 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 193 through 298 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 299 through 334 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 335 through 375 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 376 through 398 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 399 through 417 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 11 through 38 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 39 through 80 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 81 through 153 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 154 through 214 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 215 through 264 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 265 through 298 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 299 through 334 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 335 through 398 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 399 through 417 )

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