PDB-6f5v: Crystal structure of the prephenate aminotransferase from Arabido...

ID or keywords:

Entry

Database: PDB / ID: 6f5v

Title

Crystal structure of the prephenate aminotransferase from Arabidopsis thaliana

Components

Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

Keywords

TRANSFERASE / Prephenate aminotransferase Arabidopsis thaliana

Function / homology

Function and homology information

glutamate-prephenate aminotransferase / glutamate-prephenate aminotransferase activity / aromatic amino acid family biosynthetic process, prephenate pathway / aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / embryo development ending in seed dormancy / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / chloroplast stroma ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Cobessi, D. / Robin, A. / Giustini, C. / Graindorge, M. / 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	Dec 3, 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 Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6f5v.cif.gz	648.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6f5v.ent.gz	554.2 KB	Display	PDB format
PDBx/mmJSON format	6f5v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6f5v_validation.pdf.gz	500 KB	Display	wwPDB validaton report
Full document	6f5v_full_validation.pdf.gz	518.1 KB	Display
Data in XML	6f5v_validation.xml.gz	71.2 KB	Display
Data in CIF	6f5v_validation.cif.gz	102.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f5/6f5v ftp://data.pdbj.org/pub/pdb/validation_reports/f5/6f5v	HTTPS FTP

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Related structure data

Related structure data	6f35C 6f77C C: citing same article (ref.)
Similar structure data	5wmh-2 3fsl-2 1c9c-1 4f4e-d 6tor-d 4f5i-d 1cq8-1 3ezs-d 3a9z-d 3ele-2 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: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

B: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

C: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

D: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

hetero molecules

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

1

A: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

B: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

hetero molecules

defined by author&software
Evidence: gel filtration
103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

D: Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase

hetero molecules

defined by author&software
Evidence: gel filtration
103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.470, 73.240, 103.320
Angle α, β, γ (deg.)	92.49, 87.22, 111.05
Int Tables number	1
Space group name H-M	P1

#1: Protein	Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase / AtPPA-AT / Protein MATERNAL EFFECT EMBRYO ARREST 17 Mass: 51053.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: PLP bound to lysine / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAT, AAT, MEE17, At2g22250, T26C19.9 / Production host: Escherichia coli (E. coli) References: UniProt: Q9SIE1, aspartate transaminase, aspartate-prephenate aminotransferase, glutamate-prephenate aminotransferase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₆H₈O₇
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1232 / 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: 2.27 Å³/Da / Density % sol: 45.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M Na citrate pH 4.0, 11 % PEG 4K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97967 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97967 Å / Relative weight: 1
Reflection	Resolution: 1.7→23.702 Å / Num. obs: 168766 / % possible obs: 96 % / Redundancy: 6.14 % / R_sym value: 0.064 / Net I/σ(I): 16.57
Reflection shell	Resolution: 1.7→1.74 Å / Redundancy: 3.73 % / Mean I/σ(I) obs: 2.75 / Num. unique obs: 11501 / R_sym value: 0.484 / % possible all: 88.2

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Processing

Software

Name	Version	Classification
PHENIX	1.7.3_928	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→23.702 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2012	8404	4.98 %
R_work	0.1723	-	-
obs	0.1737	168692	96 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 48.162 Å² / k_sol: 0.371 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.7182 Å²	-1.0049 Å²	1.3345 Å²
2-	-	-2.4345 Å²	0.6977 Å²
3-	-	-	6.1527 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→23.702 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12160	0	101	1232	13493

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	12883
X-RAY DIFFRACTION	f_angle_d	1.075	17608
X-RAY DIFFRACTION	f_dihedral_angle_d	14.494	4861
X-RAY DIFFRACTION	f_chiral_restr	0.068	2043
X-RAY DIFFRACTION	f_plane_restr	0.005	2258

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 (%)
1.7-1.7193	0.2587	228	0.2658	4604	X-RAY DIFFRACTION	82
1.7193-1.7395	0.3211	273	0.2722	5122	X-RAY DIFFRACTION	93
1.7395-1.7608	0.2934	287	0.2463	5326	X-RAY DIFFRACTION	95
1.7608-1.783	0.2696	276	0.2421	5325	X-RAY DIFFRACTION	95
1.783-1.8065	0.3131	294	0.2357	5207	X-RAY DIFFRACTION	95
1.8065-1.8312	0.254	276	0.2147	5398	X-RAY DIFFRACTION	95
1.8312-1.8574	0.2671	258	0.2207	5245	X-RAY DIFFRACTION	95
1.8574-1.8851	0.2572	275	0.209	5397	X-RAY DIFFRACTION	95
1.8851-1.9145	0.2232	269	0.1904	5252	X-RAY DIFFRACTION	95
1.9145-1.9459	0.2281	245	0.1907	5435	X-RAY DIFFRACTION	96
1.9459-1.9794	0.2295	289	0.1892	5292	X-RAY DIFFRACTION	96
1.9794-2.0154	0.2359	298	0.1843	5330	X-RAY DIFFRACTION	96
2.0154-2.0542	0.2131	274	0.1783	5320	X-RAY DIFFRACTION	96
2.0542-2.0961	0.2201	303	0.182	5404	X-RAY DIFFRACTION	96
2.0961-2.1416	0.2189	318	0.1834	5329	X-RAY DIFFRACTION	97
2.1416-2.1914	0.2029	242	0.1742	5340	X-RAY DIFFRACTION	97
2.1914-2.2462	0.2076	284	0.1725	5455	X-RAY DIFFRACTION	97
2.2462-2.3068	0.2271	277	0.1701	5329	X-RAY DIFFRACTION	97
2.3068-2.3747	0.1942	283	0.1694	5433	X-RAY DIFFRACTION	97
2.3747-2.4512	0.2179	278	0.1728	5390	X-RAY DIFFRACTION	97
2.4512-2.5387	0.217	305	0.1737	5405	X-RAY DIFFRACTION	97
2.5387-2.6403	0.2293	288	0.177	5389	X-RAY DIFFRACTION	97
2.6403-2.7603	0.205	305	0.1739	5386	X-RAY DIFFRACTION	97
2.7603-2.9055	0.1969	293	0.1667	5455	X-RAY DIFFRACTION	98
2.9055-3.0872	0.2142	254	0.1695	5461	X-RAY DIFFRACTION	98
3.0872-3.325	0.189	278	0.1641	5455	X-RAY DIFFRACTION	98
3.325-3.6585	0.1728	285	0.1561	5482	X-RAY DIFFRACTION	98
3.6585-4.1854	0.1752	294	0.1451	5439	X-RAY DIFFRACTION	98
4.1854-5.2636	0.1384	272	0.1458	5470	X-RAY DIFFRACTION	98
5.2636-23.7039	0.177	303	0.1664	5413	X-RAY DIFFRACTION	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	6.8068	8.1913	-2.9956	2.0092	-3.7803	1.4674	0.1423	0.0683	0.0201	-0.0847	0.0096	-0.0623	0.0391	0.0787	-0.1413	0.544	0.0613	0.0628	0.2955	0.0045	0.3492	18.6007	42.4918	-4.6904
2	1.1381	-0.0806	0.1658	1.5455	-0.3748	1.1973	0.0158	-0.0097	0.1653	0.0326	-0.0719	-0.1182	-0.1867	-0.0212	0.0451	0.1141	0.0077	-0.0098	0.0699	-0.0127	0.1162	15.2509	50.39	17.2203
3	2.6578	0.3926	0.573	2.2164	-1.2582	4.434	-0.0339	0.5134	0.3164	-0.4042	-0.0488	-0.2491	-0.4395	0.119	0.0734	0.3218	0.0415	0.0531	0.1904	0.0476	0.2005	18.6191	64.4852	-5.9064
4	6.9017	-5.8342	3.6903	6.0224	-4.4366	3.5641	-0.2546	-0.2383	0.1346	0.1886	0.0347	-0.2176	0.0905	0.1828	0.2271	0.2132	0.0046	0.044	0.2418	0.0022	0.3434	11.7978	27.1745	27.2812
5	1.0828	-0.1256	0.0062	1.2719	-0.3723	0.5411	0.0493	0.0767	-0.0935	-0.3159	-0.1751	-0.2842	0.2112	0.1338	0.1041	0.2168	0.0819	0.0737	0.1292	0.0388	0.2224	28.5663	22.2629	9.1167
6	2.8699	1.2767	-0.6821	1.6814	-0.7605	1.3357	0.0383	-0.4012	-0.1421	-0.0212	-0.2639	-0.3609	0.1738	0.2448	0.2065	0.1334	0.0291	0.0233	0.1595	0.0464	0.2221	26.9669	9.3213	32.4317
7	2.0452	-2.7609	0.7533	3.719	-1.0176	0.2771	0.016	-0.0278	0.097	0.1015	0.1032	-0.0407	-0.0231	-0.0382	-0.1045	0.6445	-0.1077	0.1715	0.781	-0.1658	0.3693	21.9465	58.72	77.8432
8	0.8302	0.2651	0.1698	0.9248	0.3455	0.1366	0.0447	-0.1872	-0.0461	0.0534	0.0001	-0.0726	0.0352	0.0735	-0.0383	0.169	-0.0331	0.001	0.3672	-0.0403	0.1	30.5215	53.6653	51.0425
9	0.7506	-0.1232	0.0341	0.8415	0.0218	0.3779	0.1148	-0.2097	-0.053	0.148	-0.1423	0.256	0.138	-0.2866	0.0277	0.2241	-0.1491	0.0189	0.5325	-0.0819	0.1791	13.1593	51.4338	56.5545
10	2.7482	0.0466	-2.4033	3.0186	-2.45	7.7342	-0.0858	-0.2623	-0.405	0.3894	0.0207	0.1641	0.6613	-0.2729	0.0716	0.4052	-0.177	-0.0423	0.3483	0.0326	0.2645	25.5843	32.8974	63.2474
11	0.5345	0.0001	0.5212	0.2036	-0.1718	2.6564	-0.2032	-0.31	-0.157	0.3264	0.1051	0.0737	0.2168	-0.0465	0.0926	0.5952	-0.0706	0.0373	0.552	0.0465	0.1826	20.3843	40.6671	80.5538
12	9.9761	-0.5091	-7.6617	3.8414	-0.5334	8.608	-0.3759	-0.8677	-0.865	0.3952	-0.1029	-0.123	0.7446	0.6947	0.4844	0.7431	0.0366	-0.0973	0.5029	0.1299	0.3025	29.5928	31.1945	79.6603
13	2.8938	1.3492	-0.1324	0.7495	-0.1581	0.0706	-0.1428	0.236	0.1257	-0.2278	0.1502	0.3454	0.1482	-0.2712	-0.0046	0.3046	-0.1237	0.0057	0.4694	-0.1321	0.4001	23.2423	74.0232	43.3279
14	0.6935	0.2506	-0.0072	0.451	-0.1618	0.4278	0.1475	-0.488	0.4716	0.2753	-0.1418	0.1355	-0.1564	0.0171	0.0128	0.2655	-0.1608	0.0569	0.6394	-0.3553	0.1932	31.698	78.9564	64.2338
15	2.2712	-0.5895	0.5909	1.1413	-0.5068	1.7243	0.0288	0.2637	0.7522	0.0414	0.133	-0.0902	-0.344	0.2983	-0.1424	0.1816	-0.0648	0.0172	0.2616	-0.0177	0.5398	30.0457	90.8846	39.0469

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 24:49)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 50:333)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 334:501)
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 21:48)
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 49:332)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 333:501)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 24:49)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 50:120)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 121:307)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 308:347)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 348:404)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 405:501)
13	X-RAY DIFFRACTION	13	chain 'D' and (resseq 20:67)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 68:332)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 333:501)

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