PDB-8q5t: Nitrogenase Fe protein from Methanothermococcus thermolithotrophi...

ID or keywords:

Entry

Database: PDB / ID: 8q5t

Title

Nitrogenase Fe protein from Methanothermococcus thermolithotrophicus, monoclinic crystalline form at 2.31-A resolution

Components

Nitrogenase iron protein 1

Keywords

ELECTRON TRANSPORT / nitrogenase / electron donor / ATPase / [4Fe-4S]-cluster / electron transfer / conformational changes / methanogenic archaea / thermophile / oxidoreductase / O2-sensitivity / N2-fixation

Function / homology

Function and homology information

nitrogenase / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function

Biological species

Methanothermococcus thermolithotrophicus DSM 2095 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.31 Å

Authors

Maslac, N. / Wagner, T.

Funding support

Germany,

Switzerland, 2items

Citation

Journal: Febs J. / Year: 2024
Title: Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales.
Authors: Maslac, N. / Cadoux, C. / Bolte, P. / Murken, F. / Gu, W. / Milton, R.D. / Wagner, T.

History

Deposition	Aug 9, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 14, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8q5t.cif.gz	437.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8q5t.ent.gz	361.3 KB	Display	PDB format
PDBx/mmJSON format	8q5t.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8q5t_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	8q5t_full_validation.pdf.gz	2.7 MB	Display
Data in XML	8q5t_validation.xml.gz	42.7 KB	Display
Data in CIF	8q5t_validation.cif.gz	60.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/8q5t ftp://data.pdbj.org/pub/pdb/validation_reports/q5/8q5t	HTTPS FTP

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Related structure data

Related structure data	8q50C 8q5vC 8q5wC 8q5xC C: citing same article (ref.)
Similar structure data	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	#26 - Feb 2002 Nitrogenase similarity (9)

Deposited unit

A: Nitrogenase iron protein 1

B: Nitrogenase iron protein 1

C: Nitrogenase iron protein 1

D: Nitrogenase iron protein 1

hetero molecules

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

1

A: Nitrogenase iron protein 1

B: Nitrogenase iron protein 1

hetero molecules

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

2

C: Nitrogenase iron protein 1

D: Nitrogenase iron protein 1

hetero molecules

defined by author&software
63.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.821, 83.984, 116.598
Angle α, β, γ (deg.)	90.00, 91.14, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Nitrogenase iron protein 1 Mass: 31271.863 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: SN-1 / Tissue: / / References: UniProt: P25767
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 41.97 % / Description: The crystal was in a shape of brown plates.
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: The purified protein was crystallised at a final concentration of 6 mg/ml by spotting 0.5 ul of crystallisation solution with 0.5 ul of protein sample. Crystallisation was done anaerobically ...Details: The purified protein was crystallised at a final concentration of 6 mg/ml by spotting 0.5 ul of crystallisation solution with 0.5 ul of protein sample. Crystallisation was done anaerobically in a Coy tent containing a N2/H2 (97:3%) atmosphere. The screening was done at 20 degrees Celsius on 96-Well MRC 2-drop polystyrene (SWISSCI) plates containing 90 ul of crystallisation solution. The crystallisation solution in which crystals were obtained contained 30 % v/v 2-methyl-2,4-pentanediol, 100 mM sodium acetate, pH 4.6 and 20 mM calcium chloride.

Crystal

Density Matthews: 2.12 Å³/Da / Density % sol: 41.97 % / Description: The crystal was in a shape of brown plates.

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: The purified protein was crystallised at a final concentration of 6 mg/ml by spotting 0.5 ul of crystallisation solution with 0.5 ul of protein sample. Crystallisation was done anaerobically ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.74013 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.74013 Å / Relative weight: 1
Reflection	Resolution: 2.31→68.14 Å / Num. obs: 45087 / % possible obs: 100 % / Redundancy: 8.7 % / CC_1/2: 0.99 / R_merge(I) obs: 0.24 / R_pim(I) all: 0.085 / R_rim(I) all: 0.255 / Net I/σ(I): 5.2
Reflection shell	Resolution: 2.31→2.35 Å / Redundancy: 6.5 % / R_merge(I) obs: 1.342 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2223 / CC_1/2: 0.517 / R_pim(I) all: 0.566 / R_rim(I) all: 1.46 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.31→48.47 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.56 / Stereochemistry target values: ML
Details: Translation-libration screw was used during refinement. The model was refined with riding hydrogens that were omitted in the final deposited model.

	R_factor	Num. reflection	% reflection
R_free	0.2349	2280	5.06 %
R_work	0.1942	-	-
obs	0.1963	45074	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 37.92 Å²

Refinement step

Cycle: LAST / Resolution: 2.31→48.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8536	0	46	378	8960

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	8728
X-RAY DIFFRACTION	f_angle_d	0.874	11766
X-RAY DIFFRACTION	f_dihedral_angle_d	17.08	3325
X-RAY DIFFRACTION	f_chiral_restr	0.059	1318
X-RAY DIFFRACTION	f_plane_restr	0.007	1542

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 (%)
2.31-2.36	0.2974	130	0.2726	2664	X-RAY DIFFRACTION	100
2.36-2.41	0.3124	118	0.2567	2715	X-RAY DIFFRACTION	100
2.41-2.47	0.2947	151	0.2363	2615	X-RAY DIFFRACTION	100
2.47-2.54	0.3035	171	0.2328	2653	X-RAY DIFFRACTION	100
2.54-2.61	0.2776	143	0.2235	2656	X-RAY DIFFRACTION	100
2.61-2.7	0.2925	122	0.2239	2658	X-RAY DIFFRACTION	100
2.7-2.79	0.3193	126	0.2366	2706	X-RAY DIFFRACTION	100
2.79-2.91	0.3002	124	0.2253	2673	X-RAY DIFFRACTION	100
2.91-3.04	0.2396	126	0.2067	2671	X-RAY DIFFRACTION	100
3.04-3.2	0.2599	156	0.2038	2664	X-RAY DIFFRACTION	100
3.2-3.4	0.1971	145	0.1983	2669	X-RAY DIFFRACTION	100
3.4-3.66	0.2343	169	0.1839	2654	X-RAY DIFFRACTION	100
3.66-4.03	0.1991	160	0.1675	2661	X-RAY DIFFRACTION	100
4.03-4.61	0.1924	156	0.1513	2674	X-RAY DIFFRACTION	100
4.61-5.81	0.1845	148	0.1609	2699	X-RAY DIFFRACTION	100
5.81-48.47	0.2219	135	0.1808	2762	X-RAY DIFFRACTION	100

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	3.4718	0.3119	0.4797	3.4615	0.352	1.6056	0.0803	-0.2928	-0.0023	0.3962	-0.0264	-0.1356	0.0046	-0.1112	-0.0944	0.2438	-0.0356	-0.0008	0.1418	-0.0171	0.1768	4.1376	-2.2507	28.1718
2	1.9274	0.0351	-0.059	6.4587	0.1478	1.4658	-0.116	-0.1171	0.569	-0.1027	0.2491	0.6249	-0.1588	-0.2607	0.008	0.1936	-0.0532	-0.0097	0.234	0.0035	0.3402	-5.4599	8.4871	25.1791
3	2.3672	-0.4363	-0.3606	3.0402	-0.0839	0.9311	-0.0357	0.0724	0.1614	0.2772	-0.0021	-0.1357	-0.0068	-0.0147	0.0561	0.2071	-0.0331	-0.0206	0.1593	0.002	0.144	8.3345	6.911	29.7896
4	3.1157	0.6544	1.2851	1.498	0.5003	2.2251	0.056	0.2876	-0.1344	0.0478	-0.0288	-0.2842	0.2506	0.2283	-0.0319	0.2377	0.0012	0.0105	0.1816	0.0066	0.2726	14.8112	-7.2508	19.9807
5	2.9265	0.1135	0.9745	0.6436	0.2093	4.0648	0.0813	-0.2067	-0.0078	0.0721	0.0239	-0.0941	0.1808	0.1774	-0.0558	0.2289	0.0225	0.0157	0.1763	0.0111	0.2052	26.1651	25.2933	10.8114
6	1.3791	-0.3134	-0.1568	0.764	0.2901	2.1397	0.042	0.1021	-0.0501	-0.1109	0.018	0.0917	-0.0437	-0.1917	-0.0584	0.1963	-0.013	0.0009	0.1646	0.0435	0.2046	14.7718	24.5126	7.0419
7	2	6.311	0.9707	3.2208	0.0606	3.7782	0.3168	-0.0491	0.226	0.4515	-0.3319	0.3267	0.3144	-0.0466	-0.0973	0.5222	-0.3607	-0.1166	0.8929	-0.0348	1.0337	-0.8052	9.2063	1.8124
8	1.9787	0.0449	0.0752	2.4247	1.0778	4.1561	0.0373	0.2081	0.1111	-0.2165	0.1823	-0.3843	-0.0923	0.1031	-0.1387	0.2434	-0.0161	0.0521	0.3032	-0.0657	0.2869	1.8408	-11.8566	64.2567
9	0.5515	-0.4669	-0.4037	1.7065	-0.5101	4.4004	-0.0295	0.1216	0.0001	-0.0669	0.0627	0.1076	-0.2215	-0.3732	-0.077	0.1809	-0.0029	0.0028	0.1973	-0.0181	0.2235	-9.7447	-7.3547	68.8156
10	1.1164	0.65	0.153	1.7313	0.3529	3.3394	0.0436	-0.0053	-0.2889	0.0352	0.1367	-0.2199	0.2157	0.2613	-0.1271	0.2622	0.0239	0.0493	0.2135	-0.0463	0.2639	1.6945	-12.1877	71.7587
11	1.8221	1.5674	-0.5263	5.4415	1.2431	2.9056	-0.0069	-0.1384	0.0802	-0.0682	0.5586	-0.9739	-0.324	0.7789	-0.2129	0.2858	-0.1381	0.1167	0.5096	-0.328	0.4439	16.6897	-3.9268	67.3817
12	2.3247	-0.1698	-0.333	2.5257	-0.083	2.0193	0.1788	0.0558	-0.1291	-0.0753	0.1626	-0.4237	-0.235	0.641	0.0571	0.3541	-0.1933	0.2409	0.4494	-0.1951	0.3001	11.6083	-5.7312	61.1688
13	3.6783	-1.3179	-0.2843	1.5155	-0.0195	0.7764	0.1895	-0.2415	0.6564	-0.6065	0.2954	-0.3739	-0.4078	0.3068	-0.2874	0.6256	-0.2187	0.2168	0.4781	-0.0883	0.441	7.4301	3.1576	55.6126
14	4.3604	-1.9293	-1.3617	3.6814	0.955	2.5235	0.4522	0.6845	0.559	-0.7214	-0.0822	-0.086	-0.8282	-0.4644	-0.2568	0.5642	0.0182	0.0404	0.331	-0.0107	0.231	-6.3603	0.3962	53.099
15	2.476	0.8504	0.4388	2.1741	0.0546	0.0929	-0.0021	0.4262	0.622	-0.4477	0.2295	-0.6308	-0.3195	0.6548	-0.1095	0.311	-0.1409	0.2633	0.6598	-0.2203	0.8052	19.9467	-2.6869	59.1681
16	2.0699	-0.9793	0.1213	2.9327	-0.0301	0.8037	-0.0826	0.0087	-0.0638	0.0815	0.0559	-0.0832	0.0089	0.0235	0.0279	0.1956	0.0022	-0.0077	0.1684	0.0005	0.2133	22.4831	8.2021	83.8417
17	2.1573	0.0593	-0.348	1.4709	-0.5964	1.9586	-0.0825	0.0621	-0.0777	-0.0538	0.1036	0.2462	0.0735	-0.1738	-0.0333	0.1982	0.0406	-0.0278	0.1684	-0.0032	0.2689	5.3572	17.0593	83.1499

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 87 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 183 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 184 through 281 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 79 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 80 through 280 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 281 through 281 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 5 through 22 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 23 through 95 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 96 through 162 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 163 through 178 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 179 through 199 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 200 through 230 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 231 through 256 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 257 through 281 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 2 through 141 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 142 through 281 )

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