PDB-4q76: Crystal structure of Nfs2 C384S mutant, the plastidial cysteine d...

ID or keywords:

Entry

Database: PDB / ID: 4q76

Title

Crystal structure of Nfs2 C384S mutant, the plastidial cysteine desulfurase from Arabidopsis thaliana

Components

Cysteine desulfurase 2, chloroplastic

Keywords

TRANSFERASE / Cysteine desulfurase / AtSufE1 / Chloroplast

Function / homology

Function and homology information

selenium compound metabolic process / selenocysteine lyase / selenocysteine lyase activity / iron incorporation into metallo-sulfur cluster / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / response to selenium ion / chloroplast stroma ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Roret, T. / Didierjean, C.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: X-ray structures of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana.
Authors: Roret, T. / Pegeot, H. / Couturier, J. / Mulliert, G. / Rouhier, N. / Didierjean, C.

History

Deposition	Apr 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 10, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4q76.cif.gz	344.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4q76.ent.gz	278.9 KB	Display	PDB format
PDBx/mmJSON format	4q76.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q7/4q76 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q76	HTTPS FTP

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Related structure data

Related structure data	4q75C 1t3iS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6uy5-d 6kfy-1 1bjn-d 6o13-1 5b89-d 5zs9-1 5b87-d 5db5-d 6mrh-1 2bi3-d 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: Cysteine desulfurase 2, chloroplastic

B: Cysteine desulfurase 2, chloroplastic

94.3 kDa, 2 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)	81.718, 68.387, 87.580
Angle α, β, γ (deg.)	90.00, 94.84, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cysteine desulfurase 2, chloroplastic / NIFS-like protein / Plastid sufS-like protein / Protein AtCpNifS / Selenocysteine lyase Mass: 47161.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFS2, NIFS, At1g08490, T27G7.17 / Production host: Escherichia coli (E. coli) References: UniProt: Q93WX6, cysteine desulfurase, selenocysteine lyase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Cysteine desulfurase 2, chloroplastic / NIFS-like protein / Plastid sufS-like protein / Protein AtCpNifS / Selenocysteine lyase

Mass: 47161.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: NFS2, NIFS, At1g08490, T27G7.17 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q93WX6, cysteine desulfurase, selenocysteine lyase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.59 Å³/Da / Density % sol: 52.42 %
Crystal grow	Temperature: 278 K / Method: microbatch under oil / pH: 7.5 Details: 20% PEG3000, 0.2M sodium chloride and 0.1M HEPES pH 7.5, microbatch under oil , temperature 278K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.980111 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980111 Å / Relative weight: 1
Reflection	Resolution: 1.9→46.02 Å / Num. all: 75742 / Num. obs: 75702 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.374 / Mean I/σ(I) obs: 3.1 / Num. unique all: 10920 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
Proxima	1 Soleil	data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T3I

1t3i

Resolution: 1.9→40.713 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2616	3809	5.03 %	Scaling input intensities via French-Wilson Method
R_work	0.2331	-	-	-
all	0.2346	75742	-	-
obs	0.2346	75702	99.61 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→40.713 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6442	0	0	678	7120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6612
X-RAY DIFFRACTION	f_angle_d	0.853	8995
X-RAY DIFFRACTION	f_dihedral_angle_d	12.642	2367
X-RAY DIFFRACTION	f_chiral_restr	0.033	1011
X-RAY DIFFRACTION	f_plane_restr	0.005	1157

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.9241	0.3016	132	0.2814	2585	X-RAY DIFFRACTION	100
1.9241-1.9494	0.2918	131	0.2779	2677	X-RAY DIFFRACTION	99
1.9494-1.9761	0.3159	126	0.2545	2623	X-RAY DIFFRACTION	99
1.9761-2.0043	0.2844	134	0.2539	2637	X-RAY DIFFRACTION	99
2.0043-2.0342	0.236	146	0.2442	2642	X-RAY DIFFRACTION	99
2.0342-2.066	0.275	139	0.2466	2621	X-RAY DIFFRACTION	99
2.066-2.0999	0.2993	145	0.2469	2669	X-RAY DIFFRACTION	99
2.0999-2.1361	0.2793	143	0.2455	2641	X-RAY DIFFRACTION	99
2.1361-2.1749	0.3254	145	0.2447	2635	X-RAY DIFFRACTION	100
2.1749-2.2168	0.2895	165	0.2446	2620	X-RAY DIFFRACTION	99
2.2168-2.262	0.2334	137	0.2369	2683	X-RAY DIFFRACTION	100
2.262-2.3112	0.2644	149	0.2379	2598	X-RAY DIFFRACTION	99
2.3112-2.3649	0.2608	133	0.2376	2686	X-RAY DIFFRACTION	100
2.3649-2.4241	0.2805	146	0.2359	2658	X-RAY DIFFRACTION	100
2.4241-2.4896	0.2629	130	0.2339	2635	X-RAY DIFFRACTION	100
2.4896-2.5629	0.2372	137	0.2378	2674	X-RAY DIFFRACTION	100
2.5629-2.6456	0.2686	157	0.2364	2663	X-RAY DIFFRACTION	100
2.6456-2.7401	0.3041	156	0.2373	2653	X-RAY DIFFRACTION	100
2.7401-2.8498	0.2743	165	0.2327	2648	X-RAY DIFFRACTION	100
2.8498-2.9794	0.2642	144	0.2344	2642	X-RAY DIFFRACTION	100
2.9794-3.1365	0.2613	135	0.2225	2713	X-RAY DIFFRACTION	100
3.1365-3.3329	0.2502	131	0.2223	2660	X-RAY DIFFRACTION	100
3.3329-3.5901	0.2721	140	0.213	2695	X-RAY DIFFRACTION	100
3.5901-3.9511	0.2269	128	0.2063	2709	X-RAY DIFFRACTION	100
3.9511-4.5222	0.2353	151	0.1991	2682	X-RAY DIFFRACTION	100
4.5222-5.695	0.2215	129	0.2221	2736	X-RAY DIFFRACTION	100
5.695-40.7224	0.2695	135	0.2913	2773	X-RAY DIFFRACTION	99

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	1.8287	-0.1574	-0.0351	1.5145	0.6872	2.1117	0.0154	-0.1828	0.1068	0.1147	-0.0654	-0.2131	0.0078	0.3059	0.015	0.0997	0.0009	-0.0379	0.1366	0.0094	0.0982	35.2681	8.406	37.8156
2	1.6822	-0.789	-0.5447	1.8564	0.8545	3.0818	-0.0701	0.1067	-0.2412	0.0939	-0.0365	0.0067	0.186	0.0591	0.109	0.0978	0.0134	0.0388	0.0786	0.0391	0.1239	31.2712	-9.1015	17.5559
3	0.7296	0.3719	-0.2529	0.9549	0.2202	1.3368	-0.1057	0.0127	-0.1466	0.1883	-0.2798	0.3942	0.3281	-0.421	0.0178	0.1186	-0.0993	0.0763	0.1887	-0.1202	0.2634	13.8991	-9.6117	26.4647
4	0.7536	-0.0782	-0.0763	0.922	0.2266	0.736	-0.1153	-0.2106	-0.0966	0.3409	-0.3672	0.5705	0.2634	-0.6449	0.0182	0.1725	-0.1106	0.275	0.46	-0.2664	0.3203	3.6646	0.8277	41.3973
5	0.2837	0.0377	-0.1955	0.7615	0.5996	0.6256	-0.0763	-0.0321	-0.1629	0.1901	-0.2324	0.3089	0.3226	-0.3354	0.1242	0.1193	-0.0907	0.065	0.1769	-0.0776	0.2052	14.1228	-9.0925	25.2234
6	1.3732	-0.8938	0.417	2.5497	0.2555	0.4595	-0.221	-0.4022	0.0296	0.7262	-0.012	0.3429	0.3121	-0.0103	-0.0286	0.3573	-0.0076	0.094	0.2519	-0.0054	0.1078	22.2439	8.0791	52.5556
7	1.8784	-0.1447	-0.0699	2.6832	0.9273	1.7576	0.0879	-0.0978	0.3595	-0.0151	-0.1925	0.3336	-0.3906	-0.1894	0.1206	0.2296	-0.0115	-0.021	0.1536	-0.072	0.1637	23.3775	23.8919	42.4767
8	2.3635	-0.592	-0.1622	2.0004	0.4596	1.226	-0.0361	-0.0999	0.1348	0.1018	-0.2686	0.4009	-0.1254	-0.2525	0.1146	0.1244	0.0575	-0.0317	0.1239	-0.1017	0.1614	17.7484	14.3477	40.7061
9	2.4159	0.1755	0.1239	3.0833	0.5522	2.6264	-0.1195	-0.3332	0.2994	0.3484	0.0512	-0.1149	-0.1657	-0.058	-0.0052	0.1889	-0.0568	-0.0547	0.1909	-0.0542	0.1077	29.342	24.8292	47.9965
10	1.6733	-0.0362	0.0239	1.5165	0.6648	2.2424	0.0702	0.1032	-0.1478	-0.2497	-0.0322	-0.2622	0.0234	0.2696	0.0089	0.0957	0.0128	0.0301	0.123	0.0008	0.1231	37.9332	-7.5577	5.4519
11	1.4113	0.6698	0.2108	1.2143	0.5584	2.9707	-0.1978	-0.1315	0.071	-0.0457	-0.0054	-0.0397	-0.2598	0.1573	0.0272	0.1269	-0.001	-0.0702	0.0899	0.0282	0.0732	30.585	9.9446	24.7201
12	0.6247	-0.1037	-0.1696	1.0551	0.3838	1.1347	-0.0822	0.1335	0.0567	-0.4301	-0.2375	0.3666	-0.5384	-0.4037	0.13	0.199	0.1774	-0.1661	0.2322	-0.0958	0.2111	11.7782	5.6883	6.919
13	1.3416	1.1959	-0.0069	2.2475	0.2209	0.6095	-0.1487	0.4355	-0.0628	-0.7924	0.0345	0.1435	-0.3898	0.0328	0.0008	0.358	0.0328	-0.0382	0.2686	-0.0069	0.0896	27.6172	-7.3727	-11.3524
14	2.2079	-0.1863	0.0904	1.6838	0.4924	1.2536	-0.0314	0.1309	-0.2119	-0.1074	-0.1071	0.2792	0.1528	-0.1183	0.1199	0.0941	-0.0081	0.0139	0.1123	-0.0491	0.1074	23.6541	-17.478	-0.6004
15	2.4893	-0.41	0.0148	1.4543	0.4554	2.0809	0.0837	0.3185	-0.2296	-0.2501	-0.0078	-0.1129	0.1074	0.0381	0.0505	0.1249	0.0637	0.0602	0.1928	-0.0304	0.0903	33.7879	-23.9191	-5.5271

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and ( resseq 17:51 )	A	17 - 51
2	X-RAY DIFFRACTION	2	chain 'A' and ( resseq 52:74 )	A	52 - 74
3	X-RAY DIFFRACTION	3	chain 'A' and ( resseq 75:129 )	A	75 - 129
4	X-RAY DIFFRACTION	4	chain 'A' and ( resseq 130:226 )	A	130 - 226
5	X-RAY DIFFRACTION	5	chain 'A' and ( resseq 227:312 )	A	227 - 312
6	X-RAY DIFFRACTION	6	chain 'A' and ( resseq 313:352 )	A	313 - 352
7	X-RAY DIFFRACTION	7	chain 'A' and ( resseq 353:374 )	A	353 - 374
8	X-RAY DIFFRACTION	8	chain 'A' and ( resseq 375:407 )	A	375 - 407
9	X-RAY DIFFRACTION	9	chain 'A' and ( resseq 408:429 )	A	408 - 429
10	X-RAY DIFFRACTION	10	chain 'B' and ( resseq 17:51 )	B	17 - 51
11	X-RAY DIFFRACTION	11	chain 'B' and ( resseq 52:74 )	B	52 - 74
12	X-RAY DIFFRACTION	12	chain 'B' and ( resseq 75:312 )	B	75 - 312
13	X-RAY DIFFRACTION	13	chain 'B' and ( resseq 313:352 )	B	313 - 352
14	X-RAY DIFFRACTION	14	chain 'B' and ( resseq 353:407 )	B	353 - 407
15	X-RAY DIFFRACTION	15	chain 'B' and ( resseq 408:429 )	B	408 - 429

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