PDB-8qev: Crystal structure of ornithine transcarbamylase from Arabidopsis ...

ID or keywords:

Entry

Database: PDB / ID: 8qev

Title

Crystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with carbamoyl phosphate

Components

Ornithine transcarbamylase, chloroplastic

Keywords

TRANSFERASE / transcarbamylase / carbamoyl transferase / urea cycle / arginine biosynthesis

Function / homology

Function and homology information

ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / L-arginine biosynthetic process / chloroplast stroma / amino acid binding / chloroplast
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Nielipinski, M. / Pietrzyk-Brzezinska, A. / Sekula, B.

Funding support

Poland, 1items

Citation

Journal: Front Plant Sci / Year: 2023
Title: Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae .
Authors: Nielipinski, M. / Pietrzyk-Brzezinska, A.J. / Wlodawer, A. / Sekula, B.

History

Deposition	Sep 1, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	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 / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qev.cif.gz	384 KB	Display	PDBx/mmCIF format
PDB format	pdb8qev.ent.gz	313.4 KB	Display	PDB format
PDBx/mmJSON format	8qev.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qev_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	8qev_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8qev_validation.xml.gz	47.3 KB	Display
Data in CIF	8qev_validation.cif.gz	73.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qe/8qev ftp://data.pdbj.org/pub/pdb/validation_reports/qe/8qev	HTTPS FTP

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Related structure data

Related structure data	8qeuC C: citing same article (ref.)
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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (6)

Deposited unit

A: Ornithine transcarbamylase, chloroplastic

B: Ornithine transcarbamylase, chloroplastic

C: Ornithine transcarbamylase, chloroplastic

hetero molecules

110 kDa, 3 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)	89.247, 154.601, 191.768
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-406- SO4
2	1	B-710- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	Ornithine transcarbamylase, chloroplastic / OTCase / Ornithine carbamoyltransferase / chloroplastic Mass: 35750.836 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: OTC, At1g75330, F1B16.13 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O50039, ornithine carbamoyltransferase

#1: Protein

Ornithine transcarbamylase, chloroplastic / OTCase / Ornithine carbamoyltransferase / chloroplastic

Mass: 35750.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: OTC, At1g75330, F1B16.13
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O50039, ornithine carbamoyltransferase

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Non-polymers , 7 types, 1223 molecules

#2: Chemical	ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER Mass: 141.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₄NO₅P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1190 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 3350 26%, Lithium sulfate 0.3M, HEPES 0.1M pH 6.0, 20mM carbamoyl phosphate, cryoprotection was obtained by 25% PEG400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2023
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.55→50 Å / Num. obs: 194853 / % possible obs: 99.2 % / Redundancy: 5.51 % / CC_1/2: 0.982 / R_merge(I) obs: 0.172 / Net I/σ(I): 5.25
Reflection shell	Resolution: 1.55→1.64 Å / R_merge(I) obs: 0.957 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 30724 / CC_1/2: 0.563 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
PHENIX		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→44.67 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.948 / SU B: 4.045 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21942	1872	1 %	RANDOM
R_work	0.1844	-	-	-
obs	0.18473	187213	98.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.606 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.08 Å²	-0 Å²	0 Å²
2-	-	0.2 Å²	-0 Å²
3-	-	-	-0.28 Å²

Refinement step

Cycle: 1 / Resolution: 1.55→44.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7073	0	63	1190	8326

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	7368
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7098
X-RAY DIFFRACTION	r_angle_refined_deg	1.774	1.654	9941
X-RAY DIFFRACTION	r_angle_other_deg	0.601	1.578	16362
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.452	5	925
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.192	5	42
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.862	10	1278
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	1104
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	8483
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1633
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.683	0.244	3607
X-RAY DIFFRACTION	r_mcbond_other	0.683	0.244	3605
X-RAY DIFFRACTION	r_mcangle_it	1.108	0.43	4505
X-RAY DIFFRACTION	r_mcangle_other	1.109	0.43	4505
X-RAY DIFFRACTION	r_scbond_it	1.483	0.483	3761
X-RAY DIFFRACTION	r_scbond_other	1.483	0.484	3762
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.071	0.749	5418
X-RAY DIFFRACTION	r_long_range_B_refined	8.258	7.28	8688
X-RAY DIFFRACTION	r_long_range_B_other	8.258	7.28	8688
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.284	138	-
R_work	0.285	13288	-
obs	-	-	95.29 %

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	1.2483	0.2182	-0.7924	1.0855	0.2047	0.6276	-0.0156	-0.0762	0.0433	0.1384	0.1097	-0.1443	0.0631	0.0798	-0.0941	0.094	0.0311	-0.0433	0.1174	-0.0071	0.4255	-21.335	-25.719	34.912
2	0.4667	0.002	-0.1317	0.6134	0.2125	0.7392	0.0214	-0.014	-0.0171	0.0476	-0.0416	-0.0353	-0.0053	-0.0434	0.0202	0.1047	0.0063	0.0045	0.0978	-0.0072	0.3838	-36.014	-21.813	31.802
3	0.2971	-0.0929	-0.3649	1.0019	0.2932	0.4856	0.0512	0.0288	0.0514	-0.1493	-0.0118	-0.0297	-0.0756	-0.0507	-0.0395	0.1233	0.0027	0.0105	0.0947	0.0047	0.4101	-36.226	-11.808	20.585
4	0.3563	-0.3261	-0.0974	1.2054	0.1877	0.1235	0.0266	0.0046	0.0003	-0.0221	0.0262	-0.0953	-0.0111	0.0411	-0.0527	0.0994	0.0186	0.0071	0.1064	-0.0084	0.4165	-23.008	-22.499	23.163
5	5.0536	1.7486	1.4368	1.0742	0.2011	0.5993	-0.3334	0.2249	-0.7682	-0.1651	0.4512	-0.4705	-0.0793	-0.177	-0.1178	0.1154	-0.0386	0.1167	0.3158	-0.1396	0.6169	-13.422	-34.777	15.425
6	2.6259	1.9182	1.1467	1.7331	0.6014	5.6168	-0.0619	0.1765	-0.1448	-0.1604	0.2289	-0.5772	-0.0815	0.3867	-0.167	0.0535	-0.0151	0.1907	0.1522	-0.129	0.7452	-7.549	-30.601	17.918
7	1.2507	0.8106	-0.0797	2.072	0.8516	0.5371	0.0567	0.1264	0.0493	-0.0851	0.0896	-0.3017	-0.0621	-0.0119	-0.1464	0.1577	0.0663	0.102	0.0536	-0.0404	0.5004	-19.757	-42.061	13.417
8	0.5295	0.4062	-0.5016	2.339	0.1005	0.6019	-0.088	0.0583	-0.1488	-0.2091	-0.0183	-0.0653	0.0283	-0.0831	0.1063	0.1432	0.0541	0.0085	0.0804	-0.0649	0.4553	-23.713	-44.433	11.627
9	0.7258	-0.0947	0.1036	2.0843	1.6258	1.3654	-0.0304	-0.0063	-0.1042	0.0175	-0.0333	0.0883	0.0312	0.0485	0.0636	0.118	0.0244	0.0165	0.1109	0.0035	0.3776	-30.137	-34.491	25.041
10	1.1037	0.3885	-0.2366	1.3728	-0.6652	0.325	0.1354	-0.1236	0.1772	0.1099	-0.0554	0.1564	-0.0523	0.0342	-0.08	0.1335	0.0005	0.0448	0.0561	-0.0753	0.4444	-48.541	7.693	34.901
11	0.6177	-0.1625	0.1903	0.5572	-0.3528	0.924	0.0033	-0.0587	0.0658	-0.0294	-0.0458	0.0183	0.0113	0.0575	0.0425	0.1058	0.0019	0.0123	0.0894	-0.0073	0.3938	-44.625	-6.926	31.776
12	0.5165	0.3106	-0.1263	0.5402	-0.1136	0.0831	-0.0008	0.0181	0.1014	-0.0315	0.0385	0.0703	0.0007	-0.0181	-0.0377	0.1245	0.0013	0.0015	0.0769	-0.0037	0.4331	-51.101	1.441	22.621
13	2.6659	0.2623	-0.5466	0.7287	1.095	2.4071	0.1185	0.3423	0.7136	-0.0299	0.1307	0.2005	-0.0291	0.0578	-0.2492	0.0957	0.0031	0.0198	0.0595	0.1176	0.6315	-48.377	20.756	16.721
14	1.5156	-0.1812	-0.097	0.5961	-0.7854	1.9203	0.0514	0.1997	0.1888	-0.1641	-0.0048	0.1121	0.2908	0.037	-0.0466	0.1736	-0.0364	0.0072	0.0509	0.028	0.4828	-36.623	15.07	8.252
15	6.1823	0.973	-2.8518	2.3365	1.6077	3.26	-0.2103	0.1841	0.2817	-0.0158	0.3099	0.0573	0.1523	0.2121	-0.0996	0.2347	0.1438	0.1008	0.1911	0.0971	0.4414	-28.278	17.641	11.323
16	1.3662	0.7163	-1.0247	1.0611	-0.5285	0.7863	-0.013	-0.0655	0.062	-0.036	0.0207	-0.0794	-0.0253	0.0321	-0.0077	0.1305	-0.0039	0.0066	0.0964	-0.0078	0.4048	-35.643	6.489	24.483
17	1.5435	-0.1815	0.4427	1.9826	0.9626	0.6525	-0.0162	-0.2362	-0.1927	0.0869	0.0516	0.0851	0.0376	-0.0595	-0.0354	0.1159	-0.022	0.0511	0.1309	0.0449	0.4	-64.003	-32.535	35.139
18	0.341	-0.1081	0.2441	0.655	-0.083	0.3853	-0.0493	-0.0181	-0.0305	0.0557	0.0212	0.0186	0.0012	0.0082	0.0281	0.1065	-0.0003	0.0084	0.0943	-0.0035	0.386	-53.224	-21.83	31.839
19	0.8764	0.0156	0.1867	0.2058	0.0732	0.1085	0.0023	0.0448	-0.0947	0.006	0.005	0.0226	0.0176	-0.0084	-0.0073	0.1078	-0.0101	0.0132	0.1038	-0.0109	0.4167	-57.303	-31.683	22.819
20	0.9683	-1.1142	-0.3296	2.3802	-0.9473	1.7184	0.0775	0.0505	-0.2549	-0.2012	-0.0329	0.3963	0.1267	-0.0608	-0.0447	0.0776	-0.0629	-0.0248	0.0741	-0.0435	0.5325	-75.43	-38.947	17.084
21	0.7428	0.8856	0.6576	2.0234	0.8235	0.6828	-0.1177	0.1673	-0.1403	-0.3619	0.1822	0.1242	-0.2191	0.1078	-0.0645	0.1832	0.0025	-0.0235	0.1752	-0.0362	0.4765	-76.85	-25.581	9.143
22	4.3338	-1.4497	-0.8528	2.6427	0.1978	1.4499	-0.1776	0.3013	0.0509	-0.0879	-0.0135	0.2437	-0.0951	-0.0244	0.1911	0.072	-0.0009	-0.0563	0.1573	-0.0034	0.454	-82.679	-20.148	11.474
23	1.0604	-0.2784	0.6203	0.6498	-0.4452	0.6261	-0.0375	0.0173	0.0408	0.0302	-0.0008	0.0781	0.0137	-0.0314	0.0383	0.1009	-0.0064	0.0083	0.1104	-0.0156	0.4054	-69.365	-20.784	24.651
24	2.3489	8.9646	3.6971	34.2174	14.1129	5.822	0.0137	0.0449	-0.1334	0.0292	0.1719	-0.4942	0.0045	0.0658	-0.1856	0.1834	0.059	-0.0196	0.2064	0.0247	0.3832	-31.921	-28.981	19.904
25	21.6639	3.3028	-7.7347	0.5056	-1.1803	2.7682	0.0803	-0.0064	0.4243	0.005	0.0199	0.0605	-0.0113	-0.004	-0.1002	0.2292	-0.0298	0.0162	0.1785	-0.0197	0.4396	-40.564	0.115	19.779
26	17.0329	-12.5795	10.4799	9.2905	-7.7398	6.448	0.0328	-0.0562	-0.1113	-0.0229	0.0395	0.08	0.0198	-0.0349	-0.0723	0.1684	-0.0992	0.1351	0.1513	-0.019	0.4735	-61.416	-21.916	19.947

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	72 - 101
2	X-RAY DIFFRACTION	2	A	102 - 136
3	X-RAY DIFFRACTION	3	A	137 - 156
4	X-RAY DIFFRACTION	4	A	157 - 242
5	X-RAY DIFFRACTION	5	A	243 - 259
6	X-RAY DIFFRACTION	6	A	260 - 277
7	X-RAY DIFFRACTION	7	A	278 - 304
8	X-RAY DIFFRACTION	8	A	305 - 332
9	X-RAY DIFFRACTION	9	A	333 - 375
10	X-RAY DIFFRACTION	10	B	72 - 101
11	X-RAY DIFFRACTION	11	B	102 - 136
12	X-RAY DIFFRACTION	12	B	137 - 242
13	X-RAY DIFFRACTION	13	B	243 - 277
14	X-RAY DIFFRACTION	14	B	278 - 311
15	X-RAY DIFFRACTION	15	B	312 - 324
16	X-RAY DIFFRACTION	16	B	325 - 375
17	X-RAY DIFFRACTION	17	C	72 - 101
18	X-RAY DIFFRACTION	18	C	102 - 136
19	X-RAY DIFFRACTION	19	C	137 - 242
20	X-RAY DIFFRACTION	20	C	243 - 277
21	X-RAY DIFFRACTION	21	C	278 - 311
22	X-RAY DIFFRACTION	22	C	312 - 324
23	X-RAY DIFFRACTION	23	C	325 - 375
24	X-RAY DIFFRACTION	24	A	401
25	X-RAY DIFFRACTION	25	B	401
26	X-RAY DIFFRACTION	26	C	402

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 7 types, 1223 molecules

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-Protein , 1 types, 3 molecules ABC

-Non-polymers , 7 types, 1223 molecules

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-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 3 molecules ABC

-
Non-polymers , 7 types, 1223 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi