PDB-6vss: Arginase from Medicago truncatula

ID or keywords:

Entry

Database: PDB / ID: 6vss

Title

Arginase from Medicago truncatula

Components

Arginase

Keywords

HYDROLASE / arginine amidinohydrolase / ureohydrolase / agmatinase / agmatine amidinohydrolase

Function / homology

Function and homology information

agmatinase / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / protein hexamerization / mitochondrion / metal ion binding
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Sekula, B.

Funding support

United States, 1items

Citation

Journal: Front Plant Sci / Year: 2020
Title: The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases.
Authors: Sekula, B.

History

Deposition	Feb 11, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	Aug 19, 2020	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	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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PDBx/mmCIF format	6vss.cif.gz	724.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6vss.ent.gz	605 KB	Display	PDB format
PDBx/mmJSON format	6vss.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vs/6vss ftp://data.pdbj.org/pub/pdb/validation_reports/vs/6vss	HTTPS FTP

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Related structure data

Related structure data	6vstC 6vsuC 3lhlS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vst-2 6vst-1 6vsu-3 6vsu-2 6vsu-1 6vsu-4 5wxu-d 7c8z-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: Arginase

B: Arginase

C: Arginase

D: Arginase

E: Arginase

F: Arginase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	79.331, 142.907, 90.045
Angle α, β, γ (deg.)	90.000, 115.900, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Arginase / Arginase family protein / Putative arginase Mass: 37523.488 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Tissue: leaves / Gene: 11420737, MTR_4g024960, MtrunA17_Chr4g0011501 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7JFU5, arginase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H₂O
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: 2.04 Å³/Da / Density % sol: 39.69 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 55 mM CaCl2, 55 mM MgCl2, 80 mM HEPES/MOPS buffer at pH 7.5, 30% ethylene glycol, 15 % polyethylene glycol 8000

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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: 0.9793 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.93→44.55 Å / Num. obs: 130001 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.075 / Net I/σ(I): 10.9
Reflection shell	Resolution: 1.93→2.04 Å / R_merge(I) obs: 0.626 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 20449 / CC_1/2: 0.744 / % possible all: 93.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.25	data extraction
XDS	VERSION May 1, 2016	data reduction
XSCALE	VERSION May 1, 2016	data scaling
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LHL

3lhl

Resolution: 1.93→44.55 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.943 / SU B: 11.17 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2184	1040	0.8 %	RANDOM
R_work	0.1822	-	-	-
obs	0.1825	128959	95.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 102.14 Å² / B_iso mean: 33.82 Å² / B_iso min: 13.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.47 Å²	-0 Å²	-0.6 Å²
2-	-	4.13 Å²	0 Å²
3-	-	-	-1.42 Å²

Refinement step

Cycle: final / Resolution: 1.93→44.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14709	0	12	550	15271
B_iso mean	-	-	32.38	39.09	-
Num. residues	-	-	-	-	1905

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	15069
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	14238
X-RAY DIFFRACTION	r_angle_refined_deg	1.893	1.638	20321
X-RAY DIFFRACTION	r_angle_other_deg	1.433	1.58	32937
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.029	5	1903
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.793	21.13	832
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.687	15	2574
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.435	15	141
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1925
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	17012
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3151

LS refinement shell

Resolution: 1.93→1.978 Å / R_factor R_free error: 0

	R_factor	Num. reflection	% reflection
R_free	0.356	72	-
R_work	0.333	9047	-
obs	-	-	91.69 %

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	4.8593	-1.4812	-2.9222	0.486	0.7424	2.7665	-0.0512	-0.2883	-0.2623	-0.0004	0.1038	0.0692	0.0301	0.0125	-0.0527	0.2208	0.0603	0.0107	0.058	0.0564	0.2006	0.8508	20.5083	72.7975
2	0.7305	0.1591	0.2088	0.2424	0.0802	0.4976	-0.077	0.0461	-0.1212	-0.0179	0.0091	0.1353	0.0987	0.04	0.0679	0.1432	0.0275	-0.0052	0.1058	-0.0022	0.1747	8.1864	31.8264	58.8251
3	0.3406	0.3131	-0.1042	0.4605	-0.0057	0.3941	-0.0069	-0.0949	-0.0008	0.0424	0.0734	-0.0328	0.0378	0.1052	-0.0665	0.0997	0.0416	-0.0455	0.1915	0.01	0.112	15.9199	40.3762	72.275
4	1.1434	-0.2032	0.221	0.8561	0.0778	0.0784	-0.0463	0.0081	-0.0377	-0.1383	0.0722	0.0263	-0.0231	0.0609	-0.0259	0.1319	0.0127	-0.0069	0.1727	0.0068	0.0951	12.9903	42.3739	57.4449
5	3.2846	-1.8271	2.3158	1.308	-1.7915	2.5123	0.1609	-0.1047	0.2154	0.0759	0.0007	0.0775	-0.1415	0.083	-0.1617	0.2261	-0.0238	0.0288	0.0398	-0.0624	0.2223	-5.3886	88.6089	69.1153
6	0.6326	0.0073	0.0236	0.0805	0.0333	1.0516	0.0257	-0.0679	0.0492	0.0598	0.0035	0.0754	-0.0205	-0.0179	-0.0293	0.1611	-0.0143	-0.0157	0.0833	-0.0269	0.1454	4.3806	71.7091	65.8535
7	0.7598	0.0275	-0.1312	0.1011	-0.0372	0.7502	0.0118	0.0623	0.1545	-0.0098	0.0103	0.0176	-0.131	0.0716	-0.0221	0.1658	-0.0593	-0.0063	0.0378	-0.002	0.1958	6.6648	85.0657	55.4013
8	0.0972	0.0857	-0.096	0.4093	0.2857	0.584	-0.0025	-0.0157	0.0496	-0.005	0.0243	0.0265	0.0297	0.135	-0.0219	0.122	-0.0335	-0.0021	0.1427	-0.0035	0.1568	15.1185	71.182	52.924
9	0.5693	0.5239	0.1667	0.4927	0.1091	0.447	0.0182	0.0803	-0.092	-0.017	0.0593	-0.0809	0.0044	0.1268	-0.0776	0.1348	0.0198	-0.0101	0.1835	-0.0111	0.1099	0.6846	52.051	14.7518
10	0.4097	0.3473	-0.1235	0.6346	0.0416	0.5834	0.0203	0.0022	-0.0228	-0.0586	-0.0182	0.0894	-0.128	0.0007	-0.0021	0.0989	-0.0199	0.003	0.1865	0.012	0.1193	4.967	63.5317	28.0978
11	0.5625	0.15	0.5979	0.3218	0.1443	0.651	0.1037	0.0638	-0.0818	-0.0095	-0.0124	-0.0002	0.0658	0.0798	-0.0913	0.1123	0.0177	0.0066	0.209	-0.0231	0.102	6.8354	47.6073	17.0816
12	0.1848	0.0042	0.2568	0.0236	0.012	1.0579	0.0874	0.0409	-0.0424	0.0296	-0.0059	0.028	0.0504	0.1913	-0.0816	0.0873	0.0121	0.0002	0.2279	-0.0117	0.1184	16.9195	48.2206	32.8205
13	0.7217	-0.3539	-0.0606	0.3003	-0.1478	0.3771	-0.0078	-0.0796	-0.0557	-0.0005	0.0623	-0.0027	0.0676	-0.0046	-0.0545	0.1775	0.0049	-0.0162	0.0895	0.031	0.1342	-12.3602	25.7083	65.7873
14	0.1982	-0.0664	0.0617	0.4597	-0.3145	0.5918	0.0142	-0.0007	-0.0457	-0.0526	0.0327	0.0286	0.0637	-0.1047	-0.0469	0.1367	-0.0453	-0.0295	0.1121	0.0257	0.1632	-25.9296	30.6043	53.537
15	0.555	0.2872	-0.2401	0.1494	-0.1186	0.2415	0.0763	0.0003	0.1542	0.0375	0.0065	0.0708	-0.0008	0.0327	-0.0827	0.1457	0.0168	0.0319	0.0507	-0.0394	0.1866	-17.3377	78.5152	66.7739
16	0.3737	0.3475	-0.1967	0.5382	-0.1113	0.2791	0.024	-0.043	0.0644	-0.0311	0.0304	0.0463	0.024	-0.0559	-0.0544	0.1035	0.0074	0.0165	0.1543	-0.0096	0.1407	-29.17	63.6478	66.5895
17	0.271	0.121	-0.1265	0.0611	-0.0973	0.4849	0.0771	0.0905	0.0864	0.0248	0.0159	0.048	0.0211	-0.0383	-0.093	0.1285	0.0153	0.004	0.1822	-0.0027	0.1156	-13.2543	54.3526	14.8639
18	1.0903	1.4058	0.4103	2.1763	0.5348	0.7045	0.0392	0.0949	-0.045	0.0095	0.0295	-0.1699	0.0809	0.0256	-0.0687	0.1092	0.0014	-0.0128	0.1693	-0.0038	0.1129	-15.7398	44.6182	31.8081
19	0.4294	0.3664	-0.4523	0.5657	-0.1818	0.7309	0.0635	0.0493	0.0144	-0.0022	-0.0006	-0.032	-0.0128	-0.0426	-0.063	0.121	0.0168	-0.0055	0.1754	0.0102	0.1087	-16.3569	54.2356	18.2971
20	0.3196	-0.0333	-0.1995	0.254	0.099	0.8433	0.0934	0.0553	0.0568	0.0052	-0.0374	-0.0258	-0.1163	-0.1903	-0.056	0.0763	0.0384	-0.0058	0.2168	0.0295	0.1257	-31.3722	61.2188	28.2421
21	0.4452	-0.0313	-0.0826	0.1988	-0.0667	0.5095	0.0074	0.0013	-0.0117	0.047	0.0143	-0.0236	0.0169	-0.0648	-0.0218	0.0972	-0.0077	-0.0293	0.1808	0.0053	0.1257	-23.7891	50.7037	35.8569

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	20 - 54
2	X-RAY DIFFRACTION	2	A	55 - 116
3	X-RAY DIFFRACTION	3	A	117 - 269
4	X-RAY DIFFRACTION	4	A	270 - 338
5	X-RAY DIFFRACTION	5	B	20 - 54
6	X-RAY DIFFRACTION	6	B	55 - 116
7	X-RAY DIFFRACTION	7	B	117 - 212
8	X-RAY DIFFRACTION	8	B	213 - 338
9	X-RAY DIFFRACTION	9	C	21 - 76
10	X-RAY DIFFRACTION	10	C	77 - 116
11	X-RAY DIFFRACTION	11	C	117 - 171
12	X-RAY DIFFRACTION	12	C	172 - 338
13	X-RAY DIFFRACTION	13	D	21 - 143
14	X-RAY DIFFRACTION	14	D	144 - 338
15	X-RAY DIFFRACTION	15	E	21 - 144
16	X-RAY DIFFRACTION	16	E	145 - 338
17	X-RAY DIFFRACTION	17	F	21 - 76
18	X-RAY DIFFRACTION	18	F	77 - 101
19	X-RAY DIFFRACTION	19	F	102 - 143
20	X-RAY DIFFRACTION	20	F	144 - 269
21	X-RAY DIFFRACTION	21	F	270 - 338

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