PDB-5h8k: Crystal structure of Medicago truncatula N-carbamoylputrescine am...

ID or keywords:

Entry

Database: PDB / ID: 5h8k

Title

Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) C158S mutant

Components

N-carbamoylputrescine amidohydrolase

Keywords

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

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: 2.39 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_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5h8k.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb5h8k.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	5h8k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5h8k_validation.pdf.gz	605.8 KB	Display	wwPDB validaton report
Full document	5h8k_full_validation.pdf.gz	669.3 KB	Display
Data in XML	5h8k_validation.xml.gz	196 KB	Display
Data in CIF	5h8k_validation.cif.gz	276 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h8/5h8k ftp://data.pdbj.org/pub/pdb/validation_reports/h8/5h8k	HTTPS FTP

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Related structure data

Related structure data	5h8iC 5h8jC 5h8lC 1erzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5h8l-1 5h8j-1 5h8l-2 5h8i-1 5h8j-2 5h8i-2 5txv-1 5txv-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

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

551 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
276 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
275 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	152.531, 210.756, 208.723
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	N-carbamoylputrescine amidohydrolase Mass: 34114.594 Da / Num. of mol.: 16 / Mutation: C158S 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
#2: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3009 / Source method: isolated from a natural source / Formula: H₂O

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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 / PH range: 7

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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 23, 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: 2.39→50 Å / Num. obs: 261455 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / R_merge(I) obs: 0.139 / Net I/σ(I): 9.09
Reflection shell	Resolution: 2.39→2.54 Å / Redundancy: 5.17 % / R_merge(I) obs: 0.738 / Mean I/σ(I) obs: 2.21 / % possible all: 97.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ERZ

1erz

Resolution: 2.39→49.43 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.945 / SU B: 14.166 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21231	2615	1 %	RANDOM
R_work	0.15789	-	-	-
obs	0.15844	258839	99.25 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 57.163 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.1 Å²	-0 Å²	-0 Å²
2-	-	-0.17 Å²	0 Å²
3-	-	-	1.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.39→49.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	37528	0	310	3009	40847

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	38718
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	36841
X-RAY DIFFRACTION	r_angle_refined_deg	1.69	1.889	52309
X-RAY DIFFRACTION	r_angle_other_deg	0.809	3	84716
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.229	5	4728
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.053	24.081	1882
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.482	15	6497
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.808	15	240
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	5632
X-RAY DIFFRACTION	r_gen_planes_refined	0.02	0.021	43933
X-RAY DIFFRACTION	r_gen_planes_other	0.016	0.02	9151
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	1.435	1.44	18912
X-RAY DIFFRACTION	r_mcbond_other	1.434	1.44	18911
X-RAY DIFFRACTION	r_mcangle_it	2.268	2.15	23604
X-RAY DIFFRACTION	r_mcangle_other	2.268	2.15	23605
X-RAY DIFFRACTION	r_scbond_it	2.344	1.686	19806
X-RAY DIFFRACTION	r_scbond_other	2.344	1.686	19806
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.395	2.413	28694
X-RAY DIFFRACTION	r_long_range_B_refined	9.182	13.411	45219
X-RAY DIFFRACTION	r_long_range_B_other	9.182	13.412	45220
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.394→2.456 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	182	-
R_work	0.264	17992	-
obs	-	-	94.08 %

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	1.5722	-0.048	-0.3586	2.6667	1.3863	2.2978	-0.0477	-0.5209	0.1779	0.4407	0.0219	-0.0832	-0.0903	0.0054	0.0257	0.4487	0.0372	-0.0398	0.5465	-0.2365	0.2406	38.323	92.163	-13.381
2	2.2674	0.0391	0.1802	1.4607	0.3576	1.1613	-0.0477	-0.2857	0.155	0.0071	0.0345	-0.3266	-0.013	0.168	0.0132	0.343	-0.0048	0.0337	0.3342	-0.0605	0.1619	57.764	74.45	-34.307
3	0.9188	0.0564	0.1014	2.4253	0.0341	1.1793	-0.0855	-0.0311	0.2535	-0.401	0.0313	0.33	-0.1503	-0.1003	0.0542	0.4502	0.0447	-0.0833	0.2524	-0.0259	0.1129	23.618	74.015	-53.961
4	0.938	0.2996	0.043	2.2706	0.2752	1.0567	-0.037	0.0946	-0.1547	-0.4993	0.0613	-0.1218	0.0663	0.0776	-0.0243	0.5236	0.0414	0.0241	0.2772	-0.0233	0.0282	35.783	43.698	-61.265
5	1.6401	0.0349	0.2244	1.6324	-0.1724	1.2134	0.0744	-0.3155	-0.1325	0.1268	-0.1156	0.3166	0.0489	-0.1681	0.0412	0.3746	-0.0516	-0.0089	0.3816	0.0388	0.1056	10.764	34.997	-32.495
6	1.5992	-0.0655	0.2418	2.428	-1.0195	1.3928	0.1571	-0.3043	-0.4882	0.1456	-0.194	-0.2526	0.271	0.1522	0.0369	0.4908	-0.0312	-0.0783	0.4255	0.2281	0.3316	35.234	12.964	-26.211
7	1.4891	0.15	0.098	1.7364	0.1231	1.7516	0.2612	-0.6616	0.0552	0.5942	-0.2779	-0.3977	-0.3125	0.2427	0.0167	1.0623	-0.3435	-0.2204	1.0506	0.2271	0.2712	43.69	40.642	-0.249
8	3.1318	0.4199	0.2749	0.8238	0.8572	1.2547	0.214	-0.3614	-0.1566	0.0837	0.123	-0.7115	0.0231	0.6454	-0.337	0.8847	-0.2181	-0.3592	1.4209	0.4741	1.1506	74.279	29.327	-8.905
9	1.5943	-0.1128	-0.5636	2.5241	1.8363	2.608	0.0072	-0.2606	0.0572	0.2797	0.0317	-0.0069	-0.1215	0.0716	-0.0389	0.4569	-0.0257	0.0594	0.3078	-0.0621	0.1441	38.636	88.072	90.64
10	1.9761	0.1527	-0.2096	1.4086	0.232	1.1124	-0.0208	-0.0986	0.0873	-0.0088	0.0511	-0.2586	-0.0475	0.2144	-0.0302	0.3986	-0.0474	0.0746	0.2862	-0.0433	0.0962	58.017	70.09	69.972
11	0.8586	0.1168	0.0478	2.4298	0.024	1.1019	-0.0253	0.155	0.191	-0.3742	0.032	0.3432	-0.2417	-0.0698	-0.0067	0.5003	0.0441	-0.0455	0.2986	0.0238	0.0853	23.803	69.765	50.238
12	0.7414	0.3322	0.0771	2.092	0.2129	1.1736	-0.0722	0.1945	-0.1095	-0.4568	0.1032	-0.0641	-0.0113	0.0921	-0.031	0.4733	-0.0037	0.0201	0.3304	-0.0514	0.0184	35.708	39.286	43.168
13	1.4071	-0.3467	0.4316	1.4989	-0.1868	1.1697	-0.0525	-0.1216	-0.1242	0.1459	0.0615	0.4765	0.0026	-0.181	-0.009	0.3517	0.0019	0.0534	0.2848	0.0143	0.1994	10.375	30.93	71.796
14	1.3274	-0.2535	0.4148	1.7817	-0.7378	1.2182	0.0583	-0.039	-0.2861	0.1607	0.0256	0.0995	0.1401	0.0398	-0.0839	0.4134	0.011	0.0225	0.253	0.01	0.1424	34.675	8.86	78.502
15	1.6542	-0.3547	0.0335	1.419	0.2746	1.5858	-0.1459	-0.2573	0.1989	0.6066	0.1042	-0.1502	-0.3071	0.0716	0.0417	0.9087	0.0263	-0.0997	0.4203	-0.0118	0.1092	42.906	36.828	104.467
16	4.1277	-0.8305	0.3471	1.1055	0.6032	1.5629	-0.0429	-0.0328	0.2196	0.3135	0.0985	-0.65	-0.1677	0.5182	-0.0555	0.7054	-0.0687	-0.3216	0.6662	0.0415	0.5322	73.771	25.892	96.302

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	1 - 303
8	X-RAY DIFFRACTION	8	H	1 - 303
9	X-RAY DIFFRACTION	9	I	1 - 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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