PDB-6nic: Crystal Structure of Medicago truncatula Agmatine Iminohydrolase ...

ID or keywords:

Entry

Database: PDB / ID: 6nic

Title

Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase) in Complex with 6-aminohexanamide

Components

Porphyromonas-type peptidyl-arginine deiminase

Keywords

HYDROLASE / Polyamine metabolism / Putrescine biosynthesis

Function / homology

Function and homology information

agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process from arginine / protein-arginine deiminase activity
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Sekula, B. / Dauter, Z.

Funding support

United States, 1items

Citation

Journal: Front Plant Sci / Year: 2019
Title: Structural Study of Agmatine Iminohydrolase FromMedicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants.
Authors: Sekula, B. / Dauter, Z.

History

Deposition	Dec 27, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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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Download

PDBx/mmCIF format	6nic.cif.gz	576 KB	Display	PDBx/mmCIF format
PDB format	pdb6nic.ent.gz	478.5 KB	Display	PDB format
PDBx/mmJSON format	6nic.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/ni/6nic ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nic	HTTPS FTP

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Related structure data

Related structure data	6nibC 1vkpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5lni-1 4utj-1 1vkp-d 5ajd-3 3k12-d 5n6q-d 3n19-d 6nib-1 4utk-1 3l67-1 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: Porphyromonas-type peptidyl-arginine deiminase

B: Porphyromonas-type peptidyl-arginine deiminase

C: Porphyromonas-type peptidyl-arginine deiminase

D: Porphyromonas-type peptidyl-arginine deiminase

hetero molecules

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

1

A: Porphyromonas-type peptidyl-arginine deiminase

B: Porphyromonas-type peptidyl-arginine deiminase

hetero molecules

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

2

C: Porphyromonas-type peptidyl-arginine deiminase

D: Porphyromonas-type peptidyl-arginine deiminase

hetero molecules

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

Unit cell

Length a, b, c (Å)	142.445, 142.445, 345.429
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	C-756- HOH

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Porphyromonas-type peptidyl-arginine deiminase / Putative agmatine deiminase Mass: 41249.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Tissue: Leaves / Gene: 11445422, MTR_4g112810, MtrunA17_Chr4g0061951 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7JT50, agmatine deiminase

#1: Protein

Porphyromonas-type peptidyl-arginine deiminase / Putative agmatine deiminase

Mass: 41249.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Medicago truncatula (barrel medic) / Tissue: Leaves / Gene: 11445422, MTR_4g112810, MtrunA17_Chr4g0061951 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G7JT50, agmatine deiminase

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Non-polymers , 6 types, 787 molecules

#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-KQY / 6-aminohexanamide Mass: 130.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄N₂O
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 773 / 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: 3.07 Å³/Da / Density % sol: 59.89 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 70% of 37th condition of Morpheus Screen (04 mM Alcohols, 70 mM Buffer System 1 at pH 6.5, 35% Precipitant Mix 1)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 15, 2017
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→50.19 Å / Num. obs: 80033 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.12 / R_pim(I) all: 0.04 / R_rim(I) all: 0.13 / Net I/σ(I): 13.1
Reflection shell	Resolution: 2.2→2.38 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.726 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4106 / CC_1/2: 0.814 / R_pim(I) all: 0.29 / % possible all: 68.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
XDS	VERSION Jan 26, 2018	data reduction
STARANISO		data scaling
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1vkp

1vkp

Resolution: 2.2→50.19 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.936 / SU B: 9.562 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20416	1232	1.5 %	RANDOM
R_work	0.16543	-	-	-
obs	0.16603	78801	76.17 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 33.838 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.32 Å²	-0.16 Å²	-0 Å²
2-	-	-0.32 Å²	-0 Å²
3-	-	-	1.02 Å²

Refinement step

Cycle: 1 / Resolution: 2.2→50.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11351	0	80	773	12204

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.014	11714
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	10170
X-RAY DIFFRACTION	r_angle_refined_deg	1.865	1.652	15876
X-RAY DIFFRACTION	r_angle_other_deg	1.077	1.652	23866
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.23	5	1422
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.969	21.937	671
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.796	15	1876
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.201	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1467
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	13320
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2245
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	2.186	2.368	5712
X-RAY DIFFRACTION	r_mcbond_other	2.185	2.368	5711
X-RAY DIFFRACTION	r_mcangle_it	3.611	3.538	7126
X-RAY DIFFRACTION	r_mcangle_other	3.611	3.538	7127
X-RAY DIFFRACTION	r_scbond_it	2.462	2.634	6000
X-RAY DIFFRACTION	r_scbond_other	2.46	2.634	6000
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.974	3.825	8751
X-RAY DIFFRACTION	r_long_range_B_refined	6.355	26.632	13296
X-RAY DIFFRACTION	r_long_range_B_other	6.332	26.45	13176
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.202→2.259 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.168	6	-
R_work	0.234	268	-
obs	-	-	3.58 %

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	0.3071	0.2283	-0.0602	0.7255	-0.2884	0.1588	0.0011	-0.0437	-0.0546	-0.0062	0.0101	-0.0803	0.0234	-0.0777	-0.0112	0.0901	-0.0312	-0.0296	0.1348	0.0457	0.0822	39.2472	45.1226	95.797
2	0.7777	-0.1967	-0.6877	1.063	-0.1101	1.1024	0.0063	0.0446	0.0181	-0.0526	0.0814	0.0587	0.0881	-0.1716	-0.0877	0.0517	-0.0435	-0.0425	0.1705	0.0425	0.0699	24.7786	54.9925	90.7011
3	0.3885	0.1372	-0.2468	0.8377	-0.1821	0.4482	-0.0465	0.0145	0.0294	-0.1805	0.075	-0.0241	0.0593	-0.1222	-0.0285	0.1202	-0.028	-0.0357	0.1359	0.0204	0.0252	33.1794	55.5483	78.8484
4	1.0117	-0.362	-0.2322	0.54	-0.2397	0.3154	-0.018	0.0014	-0.0076	0.0029	-0.0053	-0.0202	-0.0232	0.005	0.0233	0.1104	0.0036	-0.0011	0.1264	0.0123	0.0606	47.9084	68.8185	84.3889
5	0.444	0.7645	-0.4096	1.3806	-0.8226	0.6324	-0.2219	0.0388	-0.1418	-0.3346	0.0697	-0.2863	0.0713	-0.0445	0.1522	0.1986	-0.0055	0.1011	0.0783	0.0095	0.1552	55.1212	44.54	80.3334
6	0.3528	0.1666	0.0026	0.1815	-0.1329	0.3481	0.035	-0.0554	-0.0309	-0.0273	-0.0568	-0.0408	-0.0236	-0.0302	0.0218	0.0986	-0.0104	-0.0135	0.1269	0.0251	0.0866	47.1275	58.5078	95.8668
7	0.2987	0.1725	0.0934	0.5763	-0.0785	0.0689	-0.0222	0.0141	-0.0026	-0.0946	0.0666	0.1006	0.0288	-0.0214	-0.0444	0.0748	-0.0825	-0.0653	0.1466	0.0406	0.077	17.2019	29.532	94.2505
8	1.9463	-0.5015	0.39	1.6992	1.9773	2.8308	0.0557	-0.2322	-0.0636	-0.1142	0.0122	-0.0234	-0.1031	-0.1191	-0.0679	0.1186	-0.0744	0.0125	0.1215	0.0346	0.0472	21.5035	32.793	111.8398
9	0.0306	-0.0636	0.1185	0.8791	-0.0416	0.5816	0.0148	-0.0183	0.0034	0.0284	0.0416	-0.0308	0.0715	-0.1046	-0.0563	0.1065	-0.0887	-0.0294	0.1022	0.0543	0.0706	23.905	18.5272	110.5165
10	0.2016	0.0759	-0.2429	1.7053	0.5969	0.6065	0.0144	0.0103	-0.0219	0.1309	-0.0831	0.2428	0.0785	-0.138	0.0686	0.1093	-0.1711	-0.0711	0.2911	0.1457	0.1398	4.926	10.5954	110.5403
11	0.2421	-0.0511	-0.1087	0.9718	-0.277	0.2119	0.0484	-0.0602	-0.0038	-0.1571	0.0476	0.0043	0.0636	-0.0999	-0.096	0.0627	-0.0954	-0.053	0.2253	0.1256	0.1346	8.7047	18.0538	96.6885
12	0.2209	-0.1105	-0.0466	0.0933	-0.1128	0.5604	-0.0351	-0.024	-0.0242	0.0371	-0.0009	0.0151	-0.0258	0.0687	0.036	0.1044	-0.0096	-0.0162	0.1227	-0.0171	0.0723	74.5209	75.4995	126.1607
13	0.6638	-0.0945	0.0411	0.0515	-0.1635	0.7728	0.0037	-0.0694	0.0276	0.015	0.0281	-0.0185	-0.0546	-0.0598	-0.0318	0.1081	0.0112	-0.0085	0.1271	-0.0051	0.0866	55.7845	77.8806	128.1579
14	0.2677	-0.1594	0.2233	0.2381	0.085	0.546	0.0227	-0.0207	-0.0147	0.0021	0.0302	0.007	0.0517	-0.0263	-0.053	0.1076	-0.0083	-0.0175	0.1063	0.0065	0.0872	58.5126	68.4544	118.9827
15	0.6942	0.0921	-0.3667	0.159	0.0451	0.3403	0.0022	0.0548	0.0555	-0.0421	0.0266	0.0353	0.0138	-0.0236	-0.0287	0.1028	0.0052	-0.0212	0.1201	0.0169	0.0691	60.316	80.7831	104.7148
16	0.3416	-0.321	-0.5807	0.9375	0.1808	1.2449	-0.0502	-0.0342	-0.0092	-0.0802	-0.0096	0.0328	0.1433	0.0681	0.0597	0.1028	0.0073	-0.0051	0.1264	-0.0129	0.0752	76.8536	69.3582	110.0796
17	0.2808	-0.152	-0.049	0.1941	0.181	0.5218	-0.0191	-0.0022	0.0027	-0.008	0.018	0.006	-0.0504	0.0685	0.0011	0.0993	-0.014	0.0008	0.1213	-0.0065	0.08	74.3847	85.053	113.5146
18	0.2863	-0.0116	0.4058	0.0283	-0.0348	0.6027	0.022	-0.0236	-0.064	0.0169	0.0522	-0.0093	-0.0232	-0.0502	-0.0742	0.1251	-0.0043	-0.0086	0.1111	0.0079	0.0707	72.0866	67.2452	149.1787
19	0.6029	-0.0981	0.5497	0.5707	-0.4099	0.6886	-0	-0.0774	-0.0413	0.0704	0.0132	-0.0393	-0.0389	-0.0565	-0.0132	0.1408	-0.0314	-0.0291	0.1199	0.0058	0.0229	84.8505	67.484	165.1445
20	0.5513	0.5331	-0.0612	1.2865	-0.5154	0.2788	0.163	-0.2468	-0.0371	0.1224	-0.1138	0.0565	-0.0117	-0.0456	-0.0492	0.1599	-0.0378	0.0158	0.1644	0.0516	0.0264	73.8143	62.1625	175.1408
21	0.0156	-0.0082	-0.0904	0.1146	-0.4259	3.9064	0.0459	-0.0474	-0.0252	-0.0855	0.1076	0.0526	0.7037	0.2519	-0.1535	0.2839	-0.0192	-0.1226	0.2169	0.0713	0.0723	73.2508	44.5482	156.4573
22	0.2053	0.1334	0.2036	0.1044	0.0563	0.7295	0.0904	-0.0955	-0.0247	0.0589	-0.0893	-0.0279	-0.0022	-0.0733	-0.0011	0.1124	-0.0272	0.0252	0.1556	0.0236	0.0514	62.6747	62.78	164.0306

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 91
2	X-RAY DIFFRACTION	2	A	92 - 119
3	X-RAY DIFFRACTION	3	A	120 - 224
4	X-RAY DIFFRACTION	4	A	225 - 285
5	X-RAY DIFFRACTION	5	A	286 - 311
6	X-RAY DIFFRACTION	6	A	312 - 374
7	X-RAY DIFFRACTION	7	B	12 - 91
8	X-RAY DIFFRACTION	8	B	92 - 119
9	X-RAY DIFFRACTION	9	B	120 - 224
10	X-RAY DIFFRACTION	10	B	225 - 285
11	X-RAY DIFFRACTION	11	B	286 - 374
12	X-RAY DIFFRACTION	12	C	12 - 91
13	X-RAY DIFFRACTION	13	C	92 - 121
14	X-RAY DIFFRACTION	14	C	122 - 191
15	X-RAY DIFFRACTION	15	C	192 - 285
16	X-RAY DIFFRACTION	16	C	286 - 319
17	X-RAY DIFFRACTION	17	C	320 - 374
18	X-RAY DIFFRACTION	18	D	11 - 165
19	X-RAY DIFFRACTION	19	D	166 - 224
20	X-RAY DIFFRACTION	20	D	225 - 285
21	X-RAY DIFFRACTION	21	D	286 - 311
22	X-RAY DIFFRACTION	22	D	312 - 374

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 787 molecules

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Experiment

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Processing

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-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 6 types, 787 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 787 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi