PDB-5gj9: Crystal structure of Arabidopsis thaliana ACO2 in complex with POA

ID or keywords:

Entry

Database: PDB / ID: 5gj9

Title

Crystal structure of Arabidopsis thaliana ACO2 in complex with POA

Components

1-aminocyclopropane-1-carboxylate oxidase 2

Keywords

OXIDOREDUCTASE / ethylene oxidase inhibitor

Function / homology

Function and homology information

aminocyclopropanecarboxylate oxidase / 1-aminocyclopropane-1-carboxylate oxidase activity / detection of ethylene stimulus / positive regulation of seed germination / ethylene biosynthetic process / plant-type cell wall /

plasmodesma / 2-oxoglutarate-dependent dioxygenase activity /

L-ascorbic acid binding / cellular response to fatty acid ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Sun, X.Z. / Li, Y.X. / He, W.R. / Ji, C.G. / Xia, P.X. / Wang, Y.C. / Du, S. / Li, H.J. / Raikhel, N. / Xiao, J.Y. / Guo, H.W.

Citation

Journal: Nat Commun / Year: 2017
Title: Pyrazinamide and derivatives block ethylene biosynthesis by inhibiting ACC oxidase.
Authors: Sun, X. / Li, Y. / He, W. / Ji, C. / Xia, P. / Wang, Y. / Du, S. / Li, H. / Raikhel, N. / Xiao, J. / Guo, H.

History

Deposition	Jun 28, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 10, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 17, 2017	Group: Structure summary
Revision 1.2	Dec 18, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	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_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5gj9.cif.gz	258.6 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	5gj9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gj/5gj9 ftp://data.pdbj.org/pub/pdb/validation_reports/gj/5gj9	HTTPS FTP

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Related structure data

Related structure data	5gjaC C: citing same article (ref.)
Similar structure data	6t6d-2 6m00-d 2abs-d 6alo-d 5qik-d 3krj-d 3hmm-d 6daz-d 6dax-d 6u0k-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
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (2)

Deposited unit

A: 1-aminocyclopropane-1-carboxylate oxidase 2

B: 1-aminocyclopropane-1-carboxylate oxidase 2

hetero molecules

69.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 1-aminocyclopropane-1-carboxylate oxidase 2

hetero molecules

defined by author
34.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 1-aminocyclopropane-1-carboxylate oxidase 2

hetero molecules

defined by author
34.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.378, 95.096, 70.145
Angle α, β, γ (deg.)	90.00, 105.91, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	1-aminocyclopropane-1-carboxylate oxidase 2 / AtACO2 Mass: 34510.129 Da / Num. of mol.: 2 / Fragment: UNP residues 1-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ACO2, EI305, At1g62380, F24O1.10 / Production host: Escherichia coli (E. coli) References: UniProt: Q41931, aminocyclopropanecarboxylate oxidase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-VGL / PYRAZINE-2-CARBOXYLIC ACID / PYRAZINOIC ACID / Pyrazinoic acid Mass: 124.097 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₄N₂O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.29 Å³/Da / Density % sol: 46.4 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 3350, citric acid

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00895 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 14, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00895 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 35745 / % possible obs: 99 % / Redundancy: 3.6 % / R_merge(I) obs: 0.067 / Net I/σ(I): 25
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.158 / Mean I/σ(I) obs: 13.2 / CC_1/2: 0.962 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data processing
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→33.729 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.69

	R_factor	Num. reflection	% reflection
R_free	0.209	2007	5.62 %
R_work	0.1532	-	-
obs	0.1564	35734	97.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.1→33.729 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4756	0	20	420	5196

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4878
X-RAY DIFFRACTION	f_angle_d	0.86	6586
X-RAY DIFFRACTION	f_dihedral_angle_d	18.1	2954
X-RAY DIFFRACTION	f_chiral_restr	0.053	708
X-RAY DIFFRACTION	f_plane_restr	0.005	864

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 (%)
2.0958-2.1482	0.2723	121	0.1847	1969	X-RAY DIFFRACTION	79
2.1482-2.2062	0.2216	136	0.1583	2390	X-RAY DIFFRACTION	99
2.2062-2.2711	0.2332	140	0.1563	2469	X-RAY DIFFRACTION	100
2.2711-2.3444	0.2003	147	0.1486	2456	X-RAY DIFFRACTION	100
2.3444-2.4282	0.2316	153	0.1606	2438	X-RAY DIFFRACTION	100
2.4282-2.5254	0.2072	133	0.1653	2455	X-RAY DIFFRACTION	100
2.5254-2.6403	0.2705	149	0.1677	2469	X-RAY DIFFRACTION	100
2.6403-2.7794	0.2309	157	0.1736	2443	X-RAY DIFFRACTION	100
2.7794-2.9535	0.2316	144	0.1745	2485	X-RAY DIFFRACTION	100
2.9535-3.1814	0.2087	143	0.1663	2457	X-RAY DIFFRACTION	100
3.1814-3.5012	0.2123	150	0.1502	2466	X-RAY DIFFRACTION	100
3.5012-4.0071	0.1806	144	0.138	2431	X-RAY DIFFRACTION	99
4.0071-5.0459	0.1709	139	0.1244	2416	X-RAY DIFFRACTION	97
5.0459-33.7333	0.1989	151	0.1511	2384	X-RAY DIFFRACTION	95

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	2.8053	0.0349	1.6888	1.172	0.659	3.7205	0.0254	-0.4056	-0.0143	0.2174	0.0022	0.4519	-0.3252	-0.7118	-0.0343	0.3438	0.0739	0.1404	0.293	0.0243	0.322	-6.5936	-8.2906	-32.2994
2	8.8864	3.775	-0.9448	3.3697	-0.298	3.6012	0.3465	-0.5155	0.0611	0.508	-0.2491	0.1402	0.0882	0.1972	-0.1218	0.4516	0.0459	0.0416	0.2392	0.0162	0.1976	14.6513	-8.3478	-16.9117
3	3.831	0.6035	-0.1021	2.3903	-1.4549	7.1929	-0.4616	0.3483	0.5341	-0.4132	-0.1693	-0.4786	-0.7579	1.4206	0.6651	0.4781	-0.1929	-0.0211	0.5445	0.046	0.4023	29.2797	2.6246	-31.5868
4	6.0411	6.0901	1.8213	7.9948	3.5512	2.973	0.2197	-0.0402	-0.7686	-0.4941	0.0329	-0.7515	0.5342	0.2038	-0.2937	0.4117	0.1001	0.0481	0.2805	0.0066	0.3627	21.4805	-18.3665	-26.5951
5	6.0935	-0.7317	6.6313	1.7738	-0.8068	8.9581	0.0314	0.3728	-0.1429	0.2932	-0.0411	0.0115	0.3846	0.2767	-0.025	0.3449	0.0284	0.1383	0.1941	0.0165	0.2469	5.5111	-18.8936	-27.8356
6	1.5799	-0.4631	0.2922	1.1015	-0.1242	2.2476	-0.1299	-0.029	0.0858	0.2919	0.0834	-0.0459	-0.3587	0.051	0.0483	0.3229	0.0074	0.0598	0.1658	0.0088	0.1441	9.8868	-6.4188	-34.6533
7	1.5645	-0.7965	-0.3503	1.6989	0.2944	1.6308	-0.1836	-0.0382	0.1509	0.3996	0.0789	0.1139	-0.1944	0.0004	0.1752	0.3131	0.0114	0.0485	0.13	0.0037	0.1798	7.759	-5.0934	-39.3619
8	0.1007	0.1676	0.4956	2.0423	1.0788	2.6392	-0.0027	-0.0036	-0.0699	0.2283	0.0741	0.1327	0.026	-0.0806	-0.0892	0.2096	0.0009	0.0793	0.1815	0.0018	0.1823	8.7229	-17.0496	-40.6483
9	4.2301	3.0171	-0.2179	6.3115	0.2074	1.8285	-0.1344	0.3608	-0.0544	-0.0165	0.1309	0.1195	0.0033	-0.0315	0.0005	0.1776	0.0241	0.0465	0.2209	-0.0299	0.1198	12.3478	-12.921	-52.1231
10	3.1402	-0.1125	0.2342	3.0663	-0.7547	2.2926	-0.0455	0.4121	-0.1982	-0.2389	-0.0239	0.4327	0.0468	-0.4234	0.037	0.144	0.0038	-0.0493	0.2291	-0.0368	0.1986	-14.4154	6.6451	-9.407
11	3.4037	-0.5991	1.086	1.9956	-0.8811	4.43	0.0784	-0.2261	-0.2176	0.1239	-0.0751	-0.2172	0.1238	0.4112	0.0159	0.1165	0.0008	-0.004	0.1839	0.008	0.2543	15.139	1.3247	0.0934
12	4.1686	-2.4478	0.389	3.3245	-0.6485	0.8454	-0.0941	-0.0335	0.6461	0.3416	0.0076	-0.6482	-0.1372	0.1298	0.0491	0.1877	-0.0376	-0.0201	0.2781	0.0002	0.3912	12.316	17.996	-0.4577
13	6.3588	1.0616	-3.8677	2.307	-0.7124	3.7142	0.1521	0.2428	0.199	-0.0898	-0.1005	-0.0694	-0.3098	-0.0189	-0.0896	0.162	-0.0084	-0.0248	0.1142	0.0131	0.1314	-1.7521	17.7789	-7.4693
14	1.4135	-0.151	-0.5168	2.5213	-0.3219	1.1226	-0.0124	-0.009	-0.069	-0.0012	-0.0341	-0.0278	0.0247	0.0413	0.035	0.0891	-0.0097	-0.0309	0.1309	0.0004	0.1112	-1.0829	5.4206	0.8236
15	2.6035	-0.9017	-1.2095	2.7591	0.3584	1.9349	0.0274	-0.0266	-0.07	0.1065	-0.0408	0.067	0.0018	-0.0295	0.0064	0.0821	-0.0218	-0.0371	0.1167	-0.0023	0.079	-5.4225	8.7078	4.4763
16	2.4096	-1.9912	0.0939	4.513	-0.2134	3.2961	-0.1513	-0.3364	0.0121	0.5764	0.0716	0.0338	-0.1753	-0.1601	0.0885	0.2502	-0.0182	0.0082	0.2063	-0.0115	0.1048	-8.0298	11.9641	17.0698

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 62 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 63 through 90 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 91 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 139 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 140 through 215 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 216 through 246 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 247 through 268 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 269 through 303 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 6 through 45 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 46 through 90 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 91 through 110 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 111 through 139 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 140 through 215 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 216 through 268 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 269 through 303 )

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