PDB-5h8i: Crystal structure of Medicago truncatula N-carbamoylputrescine am...

ID or keywords:

Entry

Database: PDB / ID: 5h8i

Title

Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with N-(dihydroxymethyl)putrescine

Components

N-carbamoylputrescine amidohydrolase

Keywords

HYDROLASE / amidase / helical octamer / alpha-beta-beta-alpha sandwich fold / intermediate

Function / homology

Function and homology information

N-carbamoylputrescine amidase / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Sekula, B. / Ruszkowski, M. / Malinska, M. / Dauter, Z.

Funding support

Poland, 1items

Citation

Journal: Front Plant Sci / Year: 2016
Title: Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants.
Authors: Sekula, B. / Ruszkowski, M. / Malinska, M. / Dauter, Z.

History

Deposition	Dec 23, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5h8i.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb5h8i.ent.gz	1.6 MB	Display	PDB format
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Validation report

Summary document	5h8i_validation.pdf.gz	621.5 KB	Display	wwPDB validaton report
Full document	5h8i_full_validation.pdf.gz	665.1 KB	Display
Data in XML	5h8i_validation.xml.gz	210.1 KB	Display
Data in CIF	5h8i_validation.cif.gz	304.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h8/5h8i ftp://data.pdbj.org/pub/pdb/validation_reports/h8/5h8i	HTTPS FTP

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Related structure data

Related structure data	5h8jC 5h8kC 5h8lC 1erzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5h8j-1 5h8j-2 5h8l-2 5h8k-2 5h8l-1 5h8k-1 3bju-d 5txv-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: N-carbamoylputrescine amidohydrolase

B: N-carbamoylputrescine amidohydrolase

C: N-carbamoylputrescine amidohydrolase

D: N-carbamoylputrescine amidohydrolase

E: N-carbamoylputrescine amidohydrolase

F: N-carbamoylputrescine amidohydrolase

G: N-carbamoylputrescine amidohydrolase

H: N-carbamoylputrescine amidohydrolase

I: N-carbamoylputrescine amidohydrolase

J: N-carbamoylputrescine amidohydrolase

K: N-carbamoylputrescine amidohydrolase

L: N-carbamoylputrescine amidohydrolase

M: N-carbamoylputrescine amidohydrolase

N: N-carbamoylputrescine amidohydrolase

O: N-carbamoylputrescine amidohydrolase

P: N-carbamoylputrescine amidohydrolase

hetero molecules

553 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-carbamoylputrescine amidohydrolase

B: N-carbamoylputrescine amidohydrolase

C: N-carbamoylputrescine amidohydrolase

D: N-carbamoylputrescine amidohydrolase

E: N-carbamoylputrescine amidohydrolase

F: N-carbamoylputrescine amidohydrolase

G: N-carbamoylputrescine amidohydrolase

H: N-carbamoylputrescine amidohydrolase

hetero molecules

defined by author&software
277 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: N-carbamoylputrescine amidohydrolase

J: N-carbamoylputrescine amidohydrolase

K: N-carbamoylputrescine amidohydrolase

L: N-carbamoylputrescine amidohydrolase

M: N-carbamoylputrescine amidohydrolase

N: N-carbamoylputrescine amidohydrolase

O: N-carbamoylputrescine amidohydrolase

P: N-carbamoylputrescine amidohydrolase

hetero molecules

defined by author&software
276 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	152.130, 211.060, 208.780
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein	N-carbamoylputrescine amidohydrolase Mass: 34130.660 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_2g086600 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: G7ITU5, N-carbamoylputrescine amidase

#1: Protein

N-carbamoylputrescine amidohydrolase

Mass: 34130.660 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Medicago truncatula (barrel medic) / Gene: MTR_2g086600 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: G7ITU5, N-carbamoylputrescine amidase

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Non-polymers , 7 types, 4463 molecules

#2: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-N2H / (4-azanylbutylamino)methanediol / N-(dihydroxymethyl)putrescine Mass: 134.177 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₅H₁₄N₂O₂
#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.: 4399 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 59.98 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG3350, 8% Tacsimate at pH 7.0, 10% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 6, 2015
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: 1.97→40 Å / Num. obs: 462097 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / R_merge(I) obs: 0.098 / Net I/σ(I): 10.45
Reflection shell	Resolution: 1.97→2.1 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 1.95 / % possible all: 91.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
XSCALE		data scaling
XDS		data reduction
BALBES		phasing
RESOLVE		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ERZ

1erz

Resolution: 1.97→39.55 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.958 / SU B: 6.695 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19299	2311	0.5 %	RANDOM
R_work	0.1579	-	-	-
obs	0.15808	459786	98.51 %	-

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: 33.576 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.14 Å²	0 Å²	0 Å²
2-	-	0.03 Å²	-0 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→39.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	37591	0	425	4399	42415

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	39094
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	37365
X-RAY DIFFRACTION	r_angle_refined_deg	1.507	1.896	52841
X-RAY DIFFRACTION	r_angle_other_deg	0.904	2.996	85935
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.765	5	4813
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.243	24.103	1889
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.287	15	6552
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.214	15	240
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	5705
X-RAY DIFFRACTION	r_gen_planes_refined	0.021	0.021	44292
X-RAY DIFFRACTION	r_gen_planes_other	0.017	0.02	9200
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	0.799	1.521	19022
X-RAY DIFFRACTION	r_mcbond_other	0.799	1.521	19021
X-RAY DIFFRACTION	r_mcangle_it	1.358	2.271	23761
X-RAY DIFFRACTION	r_mcangle_other	1.358	2.271	23762
X-RAY DIFFRACTION	r_scbond_it	1.189	1.705	20072
X-RAY DIFFRACTION	r_scbond_other	1.189	1.705	20072
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.851	2.476	29030
X-RAY DIFFRACTION	r_long_range_B_refined	7.351	14.47	47898
X-RAY DIFFRACTION	r_long_range_B_other	7.351	14.47	47899
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.971→2.022 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	141	-
R_work	0.284	27974	-
obs	-	-	81.89 %

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	1.0348	-0.0583	-0.2352	1.7984	1.2447	1.7094	-0.0222	-0.2736	0.0331	0.2765	0.0176	-0.0151	-0.0262	0.03	0.0046	0.1059	-0.0004	0.0061	0.1476	-0.0938	0.1456	38.5837	92.5808	-13.5886
2	1.5101	0.0207	-0.0454	1.0116	0.2647	0.8683	-0.0227	-0.151	0.0801	0.0154	0.0337	-0.1791	0.0011	0.1595	-0.011	0.0418	-0.0187	0.0283	0.0761	-0.0508	0.0962	57.8071	74.8429	-34.3427
3	0.6549	0.1001	0.0132	1.5465	0.0653	0.8468	-0.0211	0.0329	0.1693	-0.241	0.0081	0.2247	-0.1316	-0.0739	0.013	0.1158	0.0231	-0.0501	0.0265	-0.0006	0.0752	23.8485	74.1652	-53.9852
4	0.7046	0.087	0.0497	1.2981	0.1808	0.7871	0.017	0.1019	-0.0761	-0.275	0.0248	-0.0305	0.0419	0.0566	-0.0418	0.137	0.0212	-0.0098	0.0402	-0.0227	0.014	35.7607	43.8397	-61.0331
5	1.0571	-0.126	0.2616	0.8309	-0.1454	0.9523	0.0192	-0.1688	-0.0656	0.0526	-0.0179	0.2135	0.0418	-0.1751	-0.0014	0.0456	-0.0354	-0.0097	0.0863	0.0002	0.1047	10.8064	35.2609	-32.4314
6	0.9416	-0.1917	0.2806	1.2347	-0.5884	1.024	0.0694	-0.1224	-0.232	0.033	-0.033	-0.0187	0.2028	0.0512	-0.0364	0.1322	-0.0176	-0.0344	0.0699	0.0527	0.146	35.0205	13.3385	-25.8026
7	1.1525	-0.1707	0.1014	1.0367	0.1093	1.2027	-0.0176	-0.2723	0.1454	0.1937	0.0199	-0.1005	-0.1976	0.0859	-0.0022	0.3189	-0.0737	-0.0547	0.313	-0.0475	0.1612	43.3818	40.7796	0.2123
8	2.3903	-0.2716	0.4613	0.775	0.1552	1.2374	0.0271	-0.0389	0.1418	0.0148	-0.0064	-0.5196	-0.1262	0.4922	-0.0207	0.271	-0.0802	-0.0751	0.5274	-0.0053	0.4501	74.1229	29.7688	-8.172
9	0.952	-0.123	-0.3298	1.7085	1.2523	1.8214	0.0025	-0.2107	0.0173	0.2083	0.0249	-0.0021	-0.0745	0.0538	-0.0274	0.1084	-0.0249	0.0329	0.1045	-0.0735	0.1345	38.8437	88.111	90.5334
10	1.3337	0.0634	-0.1737	0.9848	0.1974	0.905	-0.0089	-0.11	0.06	-0.0155	0.0261	-0.148	-0.0363	0.183	-0.0172	0.0566	-0.0335	0.0416	0.0837	-0.0568	0.0904	58.0693	70.1074	69.9414
11	0.6767	0.0997	-0.0283	1.5741	0.0398	0.814	-0.0059	0.0645	0.1881	-0.2658	0.003	0.227	-0.184	-0.0687	0.0029	0.1555	0.0395	-0.0528	0.0391	0.0032	0.0847	24.0766	69.5833	50.2845
12	0.6296	0.157	0.0097	1.3474	0.1067	0.853	-0.0323	0.1142	-0.0674	-0.2959	0.0537	-0.0347	0.0124	0.0538	-0.0214	0.1199	0.0136	-0.0039	0.0599	-0.0278	0.0135	35.6913	39.1107	43.4449
13	0.9342	-0.1787	0.3064	0.8662	-0.1765	0.9064	-0.0397	-0.1066	-0.0551	0.0501	0.0284	0.2646	0.0042	-0.1544	0.0113	0.0203	0.0106	0.0136	0.0643	-0.0132	0.1212	10.3898	30.8438	71.8898
14	0.7101	-0.1635	0.2571	1.2203	-0.4637	0.9046	0.0284	-0.0464	-0.1604	0.0755	-0.0125	0.0156	0.1454	0.034	-0.0159	0.0803	0.0207	0.0075	0.04	0.0122	0.0939	34.4296	8.8408	78.8305
15	1.2759	-0.1851	0.0066	0.8384	0.222	1.1893	-0.0615	-0.2281	0.154	0.2657	0.0274	-0.093	-0.1451	0.0562	0.0341	0.2624	0.0065	-0.062	0.1805	-0.0304	0.0956	42.5753	36.547	104.8835
16	2.6738	-0.3459	0.2938	0.6807	0.3462	1.2022	-0.0495	-0.0781	0.1782	0.1339	0.1045	-0.4515	-0.1133	0.4404	-0.055	0.2088	0.0014	-0.1373	0.3676	-0.0264	0.3431	73.4083	25.7807	96.9864

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 303
2	X-RAY DIFFRACTION	2	B	1 - 303
3	X-RAY DIFFRACTION	3	C	1 - 303
4	X-RAY DIFFRACTION	4	D	1 - 303
5	X-RAY DIFFRACTION	5	E	1 - 303
6	X-RAY DIFFRACTION	6	F	1 - 303
7	X-RAY DIFFRACTION	7	G	7 - 303
8	X-RAY DIFFRACTION	8	H	5 - 303
9	X-RAY DIFFRACTION	9	I	4 - 303
10	X-RAY DIFFRACTION	10	J	1 - 303
11	X-RAY DIFFRACTION	11	K	1 - 303
12	X-RAY DIFFRACTION	12	L	1 - 303
13	X-RAY DIFFRACTION	13	M	1 - 303
14	X-RAY DIFFRACTION	14	N	1 - 303
15	X-RAY DIFFRACTION	15	O	1 - 303
16	X-RAY DIFFRACTION	16	P	1 - 303

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

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Non-polymers , 7 types, 4463 molecules

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-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

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

-
Non-polymers , 7 types, 4463 molecules

-
Details

-
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

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Yorodumi