PDB-5bsf: Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Car...

ID or keywords:

Entry

Database: PDB / ID: 5bsf

Title

Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR) in complex with NAD+

Components

Pyrroline-5-carboxylate reductase

Keywords

OXIDOREDUCTASE / proline biosynthesis / decamer / P5C / plant protein

Function / homology

Function and homology information

pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Medicago truncatula (barrel medic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Ruszkowski, M. / Nocek, B. / Forlani, G. / Dauter, Z.

Citation

Journal: Front Plant Sci / Year: 2015
Title: The structure of Medicago truncatula delta (1)-pyrroline-5-carboxylate reductase provides new insights into regulation of proline biosynthesis in plants.
Authors: Ruszkowski, M. / Nocek, B. / Forlani, G. / Dauter, Z.

History

Deposition	Jun 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2015	Group: Database references
Revision 1.2	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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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	5bsf.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb5bsf.ent.gz	859.7 KB	Display	PDB format
PDBx/mmJSON format	5bsf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5bsf_validation.pdf.gz	3.4 MB	Display	wwPDB validaton report
Full document	5bsf_full_validation.pdf.gz	3.4 MB	Display
Data in XML	5bsf_validation.xml.gz	120.6 KB	Display
Data in CIF	5bsf_validation.cif.gz	164.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bs/5bsf ftp://data.pdbj.org/pub/pdb/validation_reports/bs/5bsf	HTTPS FTP

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Related structure data

Related structure data	5bseSC 5bsgC 5bshC 2izzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5bsg-d 5bsh-d 5bse-d 5uat-1 6xoz-1 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
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: Pyrroline-5-carboxylate reductase

B: Pyrroline-5-carboxylate reductase

C: Pyrroline-5-carboxylate reductase

D: Pyrroline-5-carboxylate reductase

E: Pyrroline-5-carboxylate reductase

F: Pyrroline-5-carboxylate reductase

G: Pyrroline-5-carboxylate reductase

H: Pyrroline-5-carboxylate reductase

I: Pyrroline-5-carboxylate reductase

J: Pyrroline-5-carboxylate reductase

hetero molecules

297 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.540, 100.780, 101.610
Angle α, β, γ (deg.)	67.500, 85.860, 89.780
Int Tables number	1
Space group name H-M	P1

#1: Protein	Pyrroline-5-carboxylate reductase Mass: 28788.066 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_7g090160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) References: UniProt: G7KRM5, pyrroline-5-carboxylate reductase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1669 / 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: 2.92 Å³/Da / Density % sol: 57.91 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Morpheus screen (Molecular Dimensions) A7 solution (100 mM HEPES/MOPS buffer pH 7.5, 10% polyethylene glycol 4000, 20% glycerol, 30 mM MgCl2 and 30 mM CaCl2).

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2014

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.85→40 Å / Num. obs: 266309 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / B_iso Wilson estimate: 35.2 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.045 / R_rim(I) all: 0.053 / Χ²: 1.001 / Net I/σ(I): 17.69 / Num. measured all: 978057

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.85-1.9		3.7	0.818	0.64	1.96	72684	20253	19483	0.75	96.2
1.9-1.95			0.876	0.458	2.78	70711	19686	18989	0.535	96.5
1.95-2.01			0.922	0.355	3.59	68988	19165	18516	0.415	96.6
2.01-2.07			0.952	0.273	4.64	67085	18624	18020	0.32	96.8
2.07-2.14			0.971	0.201	6.22	65187	18063	17516	0.235	97
2.14-2.21			0.982	0.153	8.04	62968	17428	16943	0.179	97.2
2.21-2.29			0.988	0.121	9.99	61040	16930	16469	0.142	97.3
2.29-2.39			0.991	0.101	11.77	58469	16173	15765	0.118	97.5
2.39-2.49			0.993	0.082	14.4	56141	15523	15171	0.096	97.7
2.49-2.62			0.996	0.066	17.19	53707	14887	14562	0.078	97.8
2.62-2.76			0.997	0.052	21.25	50746	14086	13823	0.06	98.1
2.76-2.93			0.998	0.042	25.54	47804	13375	13120	0.05	98.1
2.93-3.13			0.998	0.035	29.99	44884	12568	12358	0.042	98.3
3.13-3.38			0.999	0.031	34.82	41412	11736	11540	0.036	98.3
3.38-3.7			0.999	0.027	40.19	37224	10700	10504	0.031	98.2
3.7-4.14			0.999	0.024	43.77	33025	9732	9501	0.029	97.6
4.14-4.78			0.999	0.021	46.85	29511	8618	8441	0.025	97.9
4.78-5.85			0.999	0.02	47.55	25645	7224	7118	0.024	98.5
5.85-8.27			0.999	0.019	50.33	20163	5586	5497	0.022	98.4
	8.27		0.998	0.022	52.91	10663	3081	2973	0.026	96.5

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.8.0073	refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2IZZ, 5BSE

2izz

5bse

Resolution: 1.85→39.13 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.96 / WR_factor R_free: 0.1691 / WR_factor R_work: 0.1501 / FOM work R set: 0.8604 / SU ML: 0.077 / SU R_free: 0.0966 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.177	2131	0.8 %	RANDOM
R_work	0.155	-	-	-
obs	0.156	264178	97.51 %	-

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 max: 150.76 Å² / B_iso mean: 41.4 Å² / B_iso min: 18.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.1 Å²	-0.42 Å²	-1.23 Å²
2-	-	-0.47 Å²	0.91 Å²
3-	-	-	1.58 Å²

Refinement step

Cycle: final / Resolution: 1.85→39.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19785	0	580	1670	22035
B_iso mean	-	-	51.25	42.75	-
Num. residues	-	-	-	-	2713

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.02	21113
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	20835
X-RAY DIFFRACTION	r_angle_refined_deg	1.864	2	28721
X-RAY DIFFRACTION	r_angle_other_deg	1.972	2.995	48072
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.998	5	2793
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.699	24.269	684
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.893	15	3555
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.244	15	111
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	3386
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	23622
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	4275
X-RAY DIFFRACTION	r_mcbond_it	2.95	2.079	11064
X-RAY DIFFRACTION	r_mcbond_other	2.949	2.079	11063
X-RAY DIFFRACTION	r_mcangle_it	4.119	3.091	13881

LS refinement shell

Resolution: 1.85→1.9 Å

	R_factor	Num. reflection	% reflection
R_free	0.271	156	-
R_work	0.281	19284	-
obs	-	-	96.28 %

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	0.5857	0.0222	-0.1276	0.3175	0.2818	0.9135	-0.0065	0.0434	0.0891	0.0861	0.2044	-0.0317	0.0121	0.0286	-0.1979	0.199	0.0354	-0.0361	0.1822	-0.0136	0.1938	68.2737	69.8422	90.6856
2	0.3455	0.0402	0.0011	0.187	0.006	0.105	0.01	-0.015	-0.0085	0.0131	0.0262	-0.0173	0.0056	-0.0046	-0.0362	0.2083	-0.0198	-0.0142	0.1926	0.0152	0.181	48.5679	61.0815	67.6807
3	0.786	-0.0541	0.1101	0.4711	-0.4263	0.5567	0.0083	-0.0826	-0.084	-0.0086	0.1265	0.0611	0.0406	-0.0162	-0.1348	0.1832	-0.0392	-0.031	0.2099	0.0765	0.1685	24.9494	43.8188	80.4331
4	0.3786	-0.0836	0.1074	0.2092	0.0586	0.0973	-0.0095	-0.0047	-0.0377	0.0149	0.0412	0.0031	-0.0145	-0.0044	-0.0317	0.2087	-0.02	-0.0133	0.1981	0.0204	0.1727	46.3751	63.4028	68.2617
5	1.1053	-0.2525	0.4426	1.0599	-0.4339	0.3228	-0.0263	0.0432	0.0461	0.1066	-0.0875	-0.1183	-0.1038	0.0086	0.1138	0.2945	-0.0241	-0.0574	0.1075	-0.0146	0.1738	57.9418	111.8124	67.1454
6	0.4493	0.031	0.0385	0.0973	-0.1283	0.2063	-0.0043	0.0167	0.0462	0.0368	-0.0102	-0.0302	-0.0202	-0.0381	0.0145	0.2059	-0.0097	-0.0035	0.1903	0.0152	0.1923	41.8586	85.8942	59.7224
7	0.7034	0.1284	-0.0604	0.1343	0.3809	1.4946	0.2406	-0.0833	0.1293	0.0542	-0.133	-0.036	0.0246	-0.4294	-0.1077	0.1134	-0.0169	0.0371	0.3548	0.0016	0.1806	11.8007	90.54	69.5609
8	0.1361	0.0281	0.0802	0.1889	-0.1886	0.2947	-0.007	0.0052	0.0217	0.0372	0.0037	-0.0236	-0.029	-0.0488	0.0033	0.2036	-0.0079	-0.0027	0.1935	0.0147	0.1932	40.5085	87.0998	57.0555
9	0.6305	0.4866	0.0772	0.7703	-0.4212	0.6694	-0.0361	-0.0458	-0.0898	-0.0667	-0.0564	-0.1701	-0.0379	-0.0648	0.0924	0.1411	0.0535	0.061	0.1492	0.05	0.2728	68.2584	104.4366	19.5087
10	0.366	0.0712	0.0979	0.157	0.0255	0.1856	0.0207	0.0311	-0.0199	0.0184	-0.0704	-0.0237	-0.0206	0.0113	0.0497	0.1716	0.0221	0.0151	0.2139	0.0331	0.1931	45.4942	87.1114	33.0435
11	0.7228	-0.3937	0.2642	1.15	-0.0309	0.1156	0.024	0.0799	0.0662	0.0625	-0.0933	0.1392	0.0249	0.0447	0.0693	0.1367	0.0252	0.0129	0.2169	-0.0022	0.2047	17.2193	96.3183	21.1778
12	0.3394	0.1318	-0.0419	0.2054	-0.0149	0.1521	0.0167	0.0074	-0.0106	-0.0125	-0.0681	-0.0066	-0.0093	-0.006	0.0514	0.1673	0.023	0.023	0.2159	0.0258	0.1954	45.1413	85.0551	30.5495
13	0.4955	-0.3354	0.2808	0.6898	-0.0121	0.2482	0.0228	0.1313	-0.1178	-0.1449	0.2407	-0.4167	-0.0783	0.1408	-0.2635	0.0716	-0.0362	0.1855	0.3715	-0.2923	0.597	82.5066	57.2086	12.8951
14	0.3214	-0.0882	0.1578	0.2791	0.0143	0.0972	0.0523	0.0546	0.0552	-0.0195	-0.0616	-0.0723	0.0374	-0.015	0.0093	0.1842	0.0426	0.0389	0.2302	0.0108	0.1779	54.1392	63.0523	24.3684
15	0.6731	0.4279	0.0748	0.3432	0.1417	1.811	-0.0892	-0.1337	0.2963	-0.1614	-0.1792	0.2221	0.2405	0.0446	0.2684	0.2775	0.1783	-0.0407	0.1795	-0.0837	0.1694	32.5964	53.6389	2.4375
16	0.1641	-0.0122	0.0322	0.2601	0.0571	0.0363	0.0727	0.0607	0.0335	-0.0016	-0.0572	-0.0461	0.0579	-0.0143	-0.0155	0.1815	0.0439	0.0348	0.2335	0.0034	0.1791	53.5873	60.0107	25.2947
17	1.2793	0.0708	0.3572	0.3572	-0.3175	0.4474	0.2186	-0.0193	-0.2031	0.0376	-0.1482	-0.0213	0.0053	0.0873	-0.0704	0.1445	-0.0002	-0.0759	0.1628	0.0236	0.2778	83.0723	36.5514	57.9823
18	0.3846	0.1397	0.091	0.0687	0.0908	0.3638	0.0797	0.0099	-0.0494	0.0092	-0.0277	-0.0339	0.0243	0.0034	-0.0519	0.1999	0.0061	-0.0233	0.1717	-0.0107	0.2153	56.0561	47.031	45.9135
19	0.5078	0.0421	-0.057	1.4593	0.2089	0.0548	0.0136	0.0107	0.0191	-0.0843	0.0355	0.1055	0.0399	0.0071	-0.0491	0.2432	-0.049	-0.1532	0.0839	0.0134	0.2296	37.428	22.1568	38.8033
20	0.5075	-0.0412	0.0435	0.0171	-0.0208	0.2933	0.0611	0.0174	-0.0624	0.0091	-0.0272	-0.0325	0.0279	-0.0359	-0.0339	0.197	-0.002	-0.0276	0.1721	-0.0034	0.2142	54.4079	46.7143	48.7262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 169
2	X-RAY DIFFRACTION	2	A	170 - 274
3	X-RAY DIFFRACTION	3	B	3 - 169
4	X-RAY DIFFRACTION	4	B	170 - 274
5	X-RAY DIFFRACTION	5	C	5 - 169
6	X-RAY DIFFRACTION	6	C	170 - 274
7	X-RAY DIFFRACTION	7	D	4 - 169
8	X-RAY DIFFRACTION	8	D	170 - 274
9	X-RAY DIFFRACTION	9	E	3 - 169
10	X-RAY DIFFRACTION	10	E	170 - 274
11	X-RAY DIFFRACTION	11	F	3 - 169
12	X-RAY DIFFRACTION	12	F	170 - 274
13	X-RAY DIFFRACTION	13	G	7 - 169
14	X-RAY DIFFRACTION	14	G	170 - 274
15	X-RAY DIFFRACTION	15	H	3 - 169
16	X-RAY DIFFRACTION	16	H	170 - 274
17	X-RAY DIFFRACTION	17	I	3 - 169
18	X-RAY DIFFRACTION	18	I	170 - 274
19	X-RAY DIFFRACTION	19	J	3 - 169
20	X-RAY DIFFRACTION	20	J	170 - 274

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