PDB-8q5w: MgADP-bound Fe protein of the molybdenum nitrogenase from Methano...

ID or keywords:

Entry

Database: PDB / ID: 8q5w

Title

MgADP-bound Fe protein of the molybdenum nitrogenase from Methanocaldococcus infernus

Components

Nitrogenase iron protein

Keywords

ELECTRON TRANSPORT /

nitrogenase /

electron donor /

ATPase / [4Fe-4S]-cluster /

electron transfer / conformational changes /

methanogenic archaea /

hyperthermophile /

oxidoreductase / O2-sensitivity / N2-fixation

Function / homology

Function and homology information

nitrogenase / carbonyl sulfide nitrogenase activity /

nitrogenase activity /

nitrogen fixation / 4 iron, 4 sulfur cluster binding /

ATP binding /

metal ion binding
Similarity search - Function

Biological species

Methanocaldococcus infernus ME (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.49 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8q5w.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb8q5w.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	8q5w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q5/8q5w ftp://data.pdbj.org/pub/pdb/validation_reports/q5/8q5w	HTTPS FTP

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Related structure data

Related structure data	8q50C 8q5tC 8q5vC 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

B: Nitrogenase iron protein

C: Nitrogenase iron protein

D: Nitrogenase iron protein

E: Nitrogenase iron protein

F: Nitrogenase iron protein

G: Nitrogenase iron protein

H: Nitrogenase iron protein

I: Nitrogenase iron protein

J: Nitrogenase iron protein

K: Nitrogenase iron protein

L: Nitrogenase iron protein

hetero molecules

383 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nitrogenase iron protein

B: Nitrogenase iron protein

hetero molecules

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

2

C: Nitrogenase iron protein

D: Nitrogenase iron protein

hetero molecules

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

3

E: Nitrogenase iron protein

F: Nitrogenase iron protein

hetero molecules

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

4

G: Nitrogenase iron protein

H: Nitrogenase iron protein

hetero molecules

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

5

I: Nitrogenase iron protein

J: Nitrogenase iron protein

hetero molecules

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

6

K: Nitrogenase iron protein

L: Nitrogenase iron protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	147.948, 156.729, 206.454
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	Nitrogenase iron protein Mass: 31148.984 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Methanocaldococcus infernus ME (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ME / Tissue: / / References: UniProt: D5VUA1

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Non-polymers , 8 types, 93 molecules

#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NO3 / NITRATE ION / Nitrate Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.27 Å³/Da / Density % sol: 62.4 % / Description: Brown pyramid
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: The purified protein was crystallised at a final concentration of 18.3 mg/ml with 2 mM ADP and 2 mM MgCl2 by spotting 0.7 ul of crystallisation solution with 0.7 ul of protein sample. ...Details: The purified protein was crystallised at a final concentration of 18.3 mg/ml with 2 mM ADP and 2 mM MgCl2 by spotting 0.7 ul of crystallisation solution with 0.7 ul of protein sample. Crystallisation was done anaerobically in a Coy tent containing 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 20 % w/v polyethylene glycol 3350, 100 mM Bis-Tris propane pH 8.5 and 200 mM sodium nitrate. Sealed plates were stored inside the same anaerobic chamber where the crystallisation was performed. The crystals in complex with MgADP were soaked in the crystallisation solution supplemented with 20% ethylene glycol prior to freezing in liquid nitrogen.

Crystal

Density Matthews: 3.27 Å³/Da / Density % sol: 62.4 % / Description: Brown pyramid

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: The purified protein was crystallised at a final concentration of 18.3 mg/ml with 2 mM ADP and 2 mM MgCl2 by spotting 0.7 ul of crystallisation solution with 0.7 ul of protein sample. ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 2.49→120.26 Å / Num. obs: 91224 / % possible obs: 91.2 % / Redundancy: 20.8 % / B_iso Wilson estimate: 79.27 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.176 / R_pim(I) all: 0.04 / R_rim(I) all: 0.18 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2.49→2.83 Å / Redundancy: 19.3 % / R_merge(I) obs: 2.314 / Mean I/σ(I) obs: 2 / Num. unique obs: 4487 / CC_1/2: 0.68 / R_pim(I) all: 0.529 / R_rim(I) all: 2.375 / % possible all: 77.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.49→49.26 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.07 / 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	0.242	4417	4.85 %
R_work	0.221	-	-
obs	0.222	91144	54.4 %

Solvent computation

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

Displacement parameters

B_iso mean: 79.27 Å²

Refinement step

Cycle: LAST / Resolution: 2.49→49.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25660	0	464	41	26165

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	26575
X-RAY DIFFRACTION	f_angle_d	1.258	35852
X-RAY DIFFRACTION	f_dihedral_angle_d	15.476	10080
X-RAY DIFFRACTION	f_chiral_restr	0.085	3942
X-RAY DIFFRACTION	f_plane_restr	0.004	4595

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 (%)
2.49-2.52	0.4044	8	0.335	77	X-RAY DIFFRACTION	2
2.52-2.55	0.5484	11	0.3796	136	X-RAY DIFFRACTION	3
2.55-2.58	0.4817	24	0.3369	214	X-RAY DIFFRACTION	4
2.58-2.61	0.3523	18	0.3559	287	X-RAY DIFFRACTION	6
2.61-2.65	0.3998	21	0.3401	349	X-RAY DIFFRACTION	7
2.65-2.68	0.6342	22	0.3737	452	X-RAY DIFFRACTION	9
2.68-2.72	0.3666	30	0.3601	564	X-RAY DIFFRACTION	11
2.72-2.76	0.2584	34	0.3284	701	X-RAY DIFFRACTION	13
2.76-2.81	0.3509	61	0.3608	934	X-RAY DIFFRACTION	18
2.81-2.85	0.4535	50	0.3527	1212	X-RAY DIFFRACTION	23
2.85-2.9	0.348	79	0.3532	1397	X-RAY DIFFRACTION	27
2.9-2.95	0.3814	73	0.3357	1606	X-RAY DIFFRACTION	30
2.95-3.01	0.3147	89	0.3221	1928	X-RAY DIFFRACTION	37
3.01-3.07	0.3393	122	0.3214	2394	X-RAY DIFFRACTION	45
3.07-3.14	0.3267	159	0.3199	2943	X-RAY DIFFRACTION	56
3.14-3.21	0.3227	181	0.3048	3594	X-RAY DIFFRACTION	68
3.21-3.29	0.3308	199	0.2936	3961	X-RAY DIFFRACTION	75
3.29-3.38	0.3346	213	0.277	4380	X-RAY DIFFRACTION	82
3.38-3.48	0.306	148	0.281	2761	X-RAY DIFFRACTION	52
3.48-3.59	0.285	272	0.2554	5200	X-RAY DIFFRACTION	98
3.59-3.72	0.284	209	0.2649	4342	X-RAY DIFFRACTION	82
3.72-3.87	0.2737	261	0.2356	5287	X-RAY DIFFRACTION	100
3.87-4.05	0.2625	223	0.2257	4141	X-RAY DIFFRACTION	78
4.05-4.26	0.2355	259	0.2051	5339	X-RAY DIFFRACTION	100
4.26-4.53	0.2119	268	0.1845	5360	X-RAY DIFFRACTION	100
4.53-4.87	0.2027	252	0.172	5354	X-RAY DIFFRACTION	100
4.87-5.36	0.2138	272	0.1894	5373	X-RAY DIFFRACTION	100
5.36-6.14	0.2279	269	0.2078	5414	X-RAY DIFFRACTION	100
6.14-7.73	0.2154	273	0.2096	5453	X-RAY DIFFRACTION	100
7.73-49.26	0.1822	317	0.1816	5574	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	3.9678	0.0101	-0.4786	3.8597	-0.9249	3.5979	0.0204	-0.5813	0.7099	1.1813	-0.3848	0.8279	-0.1334	0.1689	0.2744	0.6311	-0.0585	0.1473	0.4387	-0.0239	0.5879	-4.0885	120.6447	28.1907
2	2.6132	-0.8303	-0.3889	4.9364	-1.1139	3.1892	0.1546	-0.4986	0.1789	0.9713	-0.2233	0.7339	0.0025	0.0367	0.0764	0.7915	-0.1095	0.2102	0.5491	-0.0648	0.4277	-11.0526	104.5061	36.1773
3	1.8506	1.5611	0.0061	3.2897	-0.628	4.0228	0.3407	-0.4773	0.2334	1.8377	-0.158	1.3118	-0.3269	-0.2721	-0.1154	0.7771	-0.1074	0.3719	0.7336	-0.0497	0.7036	-17.2052	105.5373	38.8688
4	8.5987	-7.2002	-6.347	5.9197	5.8284	4.9562	-0.0239	-0.1082	0.4425	0.6067	0.0123	-0.4631	0.1006	0.3666	-0.0218	0.5946	-0.0844	0.0788	0.6879	0.0433	0.3474	-20.1099	65.126	37.0669
5	3.2486	0.753	-0.4218	6.3474	-3.2842	6.7104	0.028	0.4388	0.1908	-0.1355	0.21	1.0047	-0.0268	-0.7937	-0.2088	0.3755	-0.1161	0.0093	0.6332	-0.0243	0.411	-28.6938	59.9497	27.8415
6	2.1458	-1.5102	-0.2049	3.3984	-0.8551	2.8565	-0.0215	0.207	0.2291	0.4483	0.0346	0.328	-0.0658	-0.3209	-0.0326	0.5138	-0.0299	-0.0007	0.523	0.0013	0.3543	-19.5373	64.6578	30.4091
7	4.3101	0.1935	0.3496	1.3507	0.7613	4.8571	-0.1447	-0.5138	-0.5829	0.354	0.0941	0.0259	0.4424	0.0249	0.0593	0.6767	0.0137	0.1191	0.4683	0.1007	0.3316	-13.9252	49.3322	38.7672
8	3.4188	-1.5759	1.0736	4.4667	-0.0128	0.1633	0.0981	0.3839	0.1592	-0.3792	-0.4787	-0.4132	-0.2803	0.171	0.3509	0.5886	-0.032	0.0317	0.4826	0.0792	0.3016	6.0066	52.3062	11.0032
9	4.7177	-1.8894	-2.114	4.0594	4.8382	7.2071	-0.2113	0.0889	0.8128	0.3404	0.0172	-0.2381	-0.5146	0.1613	0.0692	0.5461	-0.0237	-0.0736	0.3335	0.1143	0.7675	15.0378	63.8687	21.0217
10	9.284	-6.1562	-4.9535	6.4258	4.5744	3.0293	0.1458	-0.5324	0.4485	-0.2997	0.2974	-0.3916	-0.1546	0.5094	-0.3593	0.5451	0.022	-0.105	0.3419	0.039	0.4185	7.1506	59.9496	19.4178
11	3.3547	-1.0342	0.6469	2.1151	-0.0408	0.7776	0.1397	0.5897	0.2478	-0.4057	-0.1662	-0.1741	0.1855	-0.2139	0.034	0.5386	-0.0182	0.0157	0.5096	0.0001	0.2008	-2.0589	59.6285	10.6704
12	5.9761	1.2079	-1.2405	2.2467	0.2623	1.8957	0.3297	0.6018	-0.3265	0.8186	-0.2679	-0.1809	-0.222	0.0849	-0.1867	0.612	0.0109	-0.0449	0.5758	-0.1459	0.3402	-8.7721	50.4245	7.8571
13	5.8101	-1.069	1.8916	1.4365	-0.2998	0.7484	0.272	0.2991	-0.6714	-0.3158	-0.0809	0.1889	0.5128	-0.1437	-0.1333	0.6891	-0.0773	0.0538	0.4471	-0.1527	0.4041	-0.2799	39.8868	11.8671
14	7.5559	0.6548	-1.9415	3.5586	-0.2496	5.1596	0.3197	0.5473	-0.5785	-0.3992	-0.3407	0.4036	0.4277	-0.7663	0.0629	0.611	-0.0006	-0.1362	0.5702	-0.1993	0.4677	-17.9107	47.2335	8.1761
15	7.047	-1.3329	-1.4578	0.7157	0.5199	1.6959	-0.0617	0.3292	0.5478	0.1168	0.1069	0.1993	-0.1615	-0.1422	-0.0412	0.603	0.0393	0.0314	0.3318	0.0126	0.3925	39.559	46.8314	15.7317
16	3.8808	0.5868	-0.3531	2.7601	0.1598	2.3034	-0.073	0.5085	-0.1662	0.0015	0.0431	0.1428	0.2568	-0.0823	0.0279	0.649	0.0665	0.0756	0.4228	-0.0871	0.3116	32.8523	36.1118	10.9624
17	3.525	1.5217	0.7044	1.6772	0.5607	1.4273	-0.0972	0.1742	-0.962	0.1497	0.0387	-0.1807	0.1934	-0.057	0.0887	0.7828	0.151	0.1931	0.4122	-0.0999	0.5926	45.1594	26.7322	11.5578
18	4.594	2.4035	-1.7543	1.8373	0.5997	4.1294	0.2525	-0.7017	-0.1663	0.1242	-0.1632	-0.2605	-0.1361	-0.1939	-0.0761	0.9071	0.0865	0.1223	0.4251	0.1031	0.6037	21.6574	21.5097	38.1695
19	1.6566	-1.5257	2.731	3.8592	-1.765	4.8125	0.0244	-0.6395	-1.3139	0.0627	0.1254	-0.2301	0.5724	-0.5201	-0.1322	0.6552	-0.0223	0.0243	0.4631	0.2004	0.7696	20.8953	16.0151	33.6624
20	5.8286	0.2311	2.5168	4.5774	-0.7867	6.8067	0.2662	-0.4521	-0.9564	0.2872	0.0215	1.01	0.1121	-0.5687	-0.2065	0.5727	-0.0462	0.073	0.4447	0.0464	0.901	10.4093	16.2992	22.6198
21	2.898	0.3662	3.0231	5.2612	-1.8367	3.4724	-0.1176	-0.3784	-0.3443	0.2372	0.4643	0.196	0.4494	-0.5618	-0.4761	0.6304	-0.0186	0.1701	0.4587	0.0175	0.6285	17.5518	20.6794	25.6695
22	4.8422	1.5992	2.4063	2.4419	0.5797	3.0902	0.047	-0.7961	-0.3795	0.5459	0.0451	0.6096	-0.4203	-0.6292	-0.1082	0.6757	0.0632	0.1787	0.4305	0.0405	0.6196	17.666	27.7016	33.6337
23	6.7893	3.4456	-2.3457	3.2487	0.4637	2.4622	0.1933	0.5974	0.3206	-0.399	0.1466	0.6513	-1.4025	-0.426	-0.2054	1.0088	0.1568	0.0921	0.558	-0.0424	0.3111	32.3527	37.1746	34.4008
24	9.1846	-5.2559	-1.9934	7.1024	2.7442	4.2962	0.4082	0.7449	0.3603	0.1296	-0.3755	-0.5675	-0.2678	-0.6255	-0.103	0.8798	0.0317	0.0175	0.5416	0.1766	0.6195	31.1984	30.4099	39.6752
25	2.1821	0.7636	0.2753	4.1844	0.2444	3.6861	0.2386	-0.3426	-0.8292	0.4314	-0.1948	-0.5585	0.5062	0.1384	-0.0243	0.6374	0.008	-0.011	0.4507	0.2253	0.6851	34.6813	16.9745	40.1299
26	6.0573	2.2812	-3.2529	6.9132	-1.4697	4.0505	0.9123	-0.6922	-0.3046	0.9674	-0.4278	-0.8405	-1.0564	0.2727	-0.4637	0.84	-0.0958	-0.0069	0.6413	0.0945	0.4719	39.1642	35.9017	40.6906
27	7.7273	1.689	-0.801	7.3294	-0.6444	0.1687	-1.0007	0.5325	-0.7896	-1.3876	0.8438	-0.4989	-0.619	-0.3734	0.1067	1.0734	0.055	0.0755	0.53	-0.1525	0.6304	66.8406	61.5689	6.851
28	2.9607	3.2373	-0.4477	9.1327	-3.0351	2.7363	0.3622	-0.2376	0.6821	-0.0902	-0.1494	0.3929	0.2321	0.1138	-0.177	0.5101	0.0892	0.0391	0.4684	-0.1272	0.4961	63.7173	71.3227	16.5702
29	2.7946	2.0103	-0.411	9.1313	-2.6834	1.929	-0.1357	0.0271	0.2612	-0.4144	0.0867	0.6034	0.4385	-0.069	0.1101	0.5794	0.0758	0.0535	0.3917	-0.1321	0.4895	60.7605	61.0986	14.3394
30	5.055	-0.5306	-2.156	3.6725	-2.1732	3.5495	-0.4292	1.2446	-0.2227	-0.7491	0.3846	-0.8899	0.0968	-0.2261	0.0074	0.9451	0.1495	0.2692	0.5424	-0.1196	0.6529	70.3452	55.709	9.9743
31	3.608	2.0674	-1.076	3.1954	-2.0917	2.7501	-0.3706	-0.5039	-0.6162	-0.7925	0.0746	-1.5412	0.4233	0.0436	0.2912	0.6212	0.1977	0.3632	0.6409	-0.2175	1.2856	78.1517	52.6255	10.6426
32	2.1361	-1.8057	-0.6559	1.8463	-0.309	2.8579	-0.4944	0.1894	-1.257	-0.0659	-1.0055	-1.9901	-0.1826	1.6101	-0.4325	0.0811	0.3493	0.881	0.7639	-0.2945	2.2736	87.8191	59.144	9.8726
33	5.3585	-0.432	-0.3244	6.3444	-1.0222	0.0885	-0.4388	0.1189	0.3538	-0.1814	0.3051	-1.9632	-0.1602	-0.0113	0.0483	0.4401	0.0372	0.1478	0.5564	-0.1143	1.033	80.358	76.0295	14.3781
34	3.1264	2.6902	-1.2649	3.3031	-0.5737	0.6227	0.1934	-0.2532	-1.2058	-1.2012	-0.3344	-2.8496	0.2945	0.0721	0.2288	0.9732	0.0487	0.5372	0.8464	-0.0856	1.9428	85.3269	49.1088	8.3565
35	2.5501	-2.551	0.5193	3.1778	-0.0862	1.7382	0.4724	-0.3899	-0.1335	1.9027	-0.481	-2.3573	1.3146	0.0007	0.032	1.7357	0.0509	-0.819	1.1385	0.1569	1.2626	79.3823	38.9753	36.235
36	5.0561	-1.6635	2.1947	1.237	1.3836	7.9662	0.0949	0.2092	-0.6401	0.7607	-0.1662	-0.6479	1.041	0.7781	-0.0568	0.8494	0.0983	-0.2216	0.6853	0.2584	1.6027	75.6316	27.6071	23.13
37	1.8912	0.0483	0.9339	4.6477	-1.6907	3.305	0.3966	-0.9742	-0.5416	1.8618	-0.4325	-1.1261	0.1947	-0.1951	-0.0105	1.1223	-0.0127	-0.332	0.762	0.1475	0.8343	70.7082	42.4279	32.3723
38	1.9409	-0.0854	-0.0332	4.1505	-0.4531	3.2235	0.0907	-0.5264	-0.2645	2.0953	-0.2449	-2.0588	-0.1179	0.5502	0.2061	1.2571	-0.1113	-0.5937	1.0915	0.1334	1.3336	81.7626	53.1245	39.9688
39	3.6788	-1.2019	-1.128	1.6463	2.6595	6.5269	-0.1403	-0.8259	0.2579	1.0133	-0.0895	-1.1657	0.2873	0.2602	0.227	0.9182	0.045	-0.4242	0.9099	0.0021	1.043	90.6442	98.6632	36.1963
40	8.2944	-0.5375	3.0161	3.3052	0.5447	3.4864	-0.3031	-0.655	0.3722	0.4222	-0.1688	-0.7684	-0.0441	0.5855	0.3848	0.5707	0.1518	-0.1281	1.0801	0.0341	1.1858	96.1625	91.5413	23.7061
41	2.1387	0.4667	-1.5883	0.0383	-0.4541	1.3	-1.0847	-0.8674	-0.3386	1.6657	0.4932	-0.7831	0.3556	0.6403	0.5158	0.9768	0.2618	-0.4501	0.9936	-0.056	1.0364	88.8417	88.8309	32.2732
42	4.5549	-1.0929	-1.3384	1.8905	-0.0834	3.6698	-0.0729	-1.3569	0.6196	1.0101	0.2846	-1.0511	-0.1892	0.5739	-0.1413	1.0766	0.0845	-0.3665	1.0596	-0.2132	0.9091	80.6746	104.497	38.4139
43	3.3491	0.3867	1.0724	3.7645	-2.9804	2.9933	-0.2296	-0.7527	0.0642	1.9672	0.5068	0.024	-0.2977	0.1702	-0.2525	1.4402	0.107	0.0021	1.097	-0.0327	0.5167	67.1312	104.9595	40.5521
44	3.5593	-1.3658	0.3139	4.3119	-0.8757	1.9043	0.1511	0.5594	0.0765	-0.1326	-0.2369	-0.3129	0.122	0.3295	0.0812	0.423	0.0427	0.1709	0.4829	-0.0058	0.4185	64.2064	104.0704	13.3365
45	1.4409	-2.029	0.1022	3.0251	0.007	0.247	0.341	0.5391	1.2824	-0.4697	-0.2111	-1.3924	0.1864	0.447	-0.0336	0.7835	-0.0332	0.4501	0.9645	0.177	1.3419	84.5095	110.0072	9.6852
46	4.675	-0.8613	-0.3034	7.8002	2.5032	5.7181	-0.1105	1.1999	-0.596	-0.3095	-0.4311	-0.0437	0.7627	-0.0324	0.4783	0.5689	-0.1689	0.0583	0.909	-0.0111	0.4609	31.2842	116.3418	6.9108
47	4.9251	-0.8746	1.2259	0.9578	-0.7636	0.5017	-0.2651	0.494	-0.4801	-0.0424	0.2305	0.0482	-0.0231	0.2101	0.0318	0.4812	-0.0826	0.1454	0.6088	-0.0498	0.3875	20.8621	115.2246	12.0121
48	7.9579	-3.478	0.2255	2.0249	0.2305	2.5549	-0.8317	-0.5221	-1.855	-0.0458	0.6881	0.2164	0.1749	0.1294	0.2525	0.639	-0.0063	0.1465	0.3975	0.1001	0.7487	26.6539	105.8044	22.7516
49	4.5253	1.1009	0.5878	1.2414	0.3625	2.5079	-0.3032	0.7263	-0.7876	-0.1215	0.1915	-0.1728	0.5203	0.1561	0.0916	0.4572	-0.0235	0.1467	0.3919	-0.0654	0.549	31.6615	107.9813	14.65
50	3.6709	1.5274	0.6098	3.4939	-1.8101	2.7177	-0.2158	0.8751	0.4289	-0.2756	0.1521	-0.0787	-0.4335	0.0089	0.0441	0.5588	-0.0994	0.0515	0.5119	0.1648	0.4209	33.6784	127.5021	10.8033
51	4.3454	2.7022	-1.2346	2.6343	-0.212	0.6885	-0.3126	0.6159	0.7787	-0.3556	0.3249	0.251	-0.2883	-0.0451	-0.0107	0.5861	0.0454	-0.1414	0.5159	0.1924	0.5267	16.5621	127.1691	12.4514
52	5.3249	0.6833	0.2017	1.8189	1.5094	2.896	-0.2057	0.6048	1.3275	-0.4086	0.4751	0.4899	-0.6312	-0.3952	-0.2454	0.7108	0.0083	0.0564	0.6833	0.3787	0.7579	32.002	138.9733	10.3411
53	7.7713	3.0829	1.9919	3.782	-0.6821	6.8318	0.3377	-0.4711	0.1162	0.6993	-0.2303	0.1455	0.2921	0.488	-0.0831	0.7288	0.01	0.0462	0.3516	-0.0312	0.4441	43.9867	134.6545	39.2048
54	5.9598	-0.7446	-4.7007	5.5239	1.0362	6.7888	0.2401	-0.4491	1.2576	-0.2258	0.0406	-0.4909	-0.5849	0.1427	-0.3032	0.4643	-0.0587	0.0637	0.381	-0.028	0.6196	45.0318	140.2947	34.9542
55	6.8994	-3.4661	-1.0073	7.9265	3.5247	6.306	1.1012	0.4161	1.0744	-1.0858	-0.381	-1.7121	-0.813	0.7759	-0.716	0.6211	-0.0574	0.2048	0.4534	0.0362	1.0188	55.7761	140.4786	24.3458
56	3.5863	1.608	-0.858	2.8665	0.1041	3.8668	0.0702	-0.3293	0.1379	0.1867	-0.1694	-0.1055	-0.2495	0.4422	0.1324	0.4968	-0.0804	0.1199	0.3705	0.0452	0.6747	51.7989	132.6345	27.5192
57	3.8396	2.0904	-1.5127	3.3898	-0.4328	3.023	0.2267	-0.3457	0.1791	0.4147	-0.0502	-0.3165	0.4697	0.4149	-0.2007	0.6496	0.0973	0.047	0.4344	0.0114	0.4369	42.295	126.1434	35.8961
58	5.4586	-2.1142	-0.926	8.0376	-0.7982	7.1188	1.0146	-0.0352	0.1561	0.2104	-0.7828	0.176	-0.3083	0.8286	-0.3004	0.7015	-0.0938	0.1037	0.4642	-0.0557	0.3901	34.5138	125.8083	40.1466
59	1.9244	0.5121	-1.2901	4.9008	-1.2816	4.8255	0.3231	-0.2437	0.5548	0.5063	-0.0678	0.4964	-0.3707	-0.0938	-0.266	0.4816	0.0478	0.0879	0.4477	-0.0317	0.456	29.5374	133.4651	40.7842
60	9.6079	0.0615	-3.5655	8.3039	0.397	6.895	-0.7935	1.309	0.5668	-1.9635	0.2208	-0.5898	0.2938	-0.392	0.2401	0.6873	0.0546	0.0369	0.3208	0.128	0.4916	0.1481	95.3573	6.0144
61	4.2146	3.6782	0.4638	6.8867	-0.1675	0.1051	-0.0731	-0.1338	-0.3984	-0.2484	-0.2871	-0.6047	0.0819	0.2705	0.3363	0.5353	0.12	0.065	0.509	0.1403	0.2963	-4.3227	85.832	12.6357
62	5.4801	4.7412	-1.1592	5.8404	1.4027	3.2193	0.1025	-0.3229	-0.4837	0.1499	-0.3331	-1.2914	-0.1955	0.2394	0.2599	0.4265	-0.0201	-0.0984	0.528	0.2008	0.6467	8.5531	87.745	23.761
63	2.574	-0.3889	0.9851	8.0634	2.7199	1.2341	0.4151	-0.1025	0.0169	0.2131	-0.1768	-1.8263	0.102	0.3082	-0.2508	0.4697	-0.0457	-0.0086	0.5109	0.2059	0.6229	8.61	88.8666	18.3004
64	1.4126	-0.7433	1.171	6.9619	0.3981	3.044	-0.2247	0.2926	-0.007	-0.1058	0.0342	-1.0797	0.1802	0.3567	0.1806	0.3858	-0.0628	0.0455	0.3728	0.1091	0.5028	5.6192	94.7104	10.9932
65	3.5526	0.6934	1.2682	3.2536	0.5551	4.2803	0.1124	0.2607	0.4322	-0.7141	-0.3102	0.1335	-0.1627	0.3019	0.1694	0.4807	0.0478	-0.0799	0.4461	0.1623	0.3246	-6.6685	104.4471	9.8635
66	9.9725	2.0927	-3.3366	4.8032	-0.0678	4.3631	0.8271	-0.035	0.1863	0.0303	-0.6672	0.0707	-0.5184	0.2364	-0.1381	0.5754	0.0754	-0.1024	0.4925	0.1122	0.4087	-11.922	100.9767	7.2485
67	1.6743	-0.8388	1.2815	3.838	-2.0813	1.8907	-0.041	-0.1213	0.1645	0.0563	0.1716	0.4779	-0.1802	-0.4058	-0.1274	0.373	0.0346	-0.0767	0.5233	-0.0098	0.4054	-16.9473	88.3371	10.8805
68	1.8946	1.2393	-0.4185	3.19	0.3124	0.5456	0.22	0.4303	0.1975	-0.8453	-0.6359	1.4146	-0.6952	-0.8395	0.1588	0.4451	0.1735	-0.1942	0.7018	0.06	0.7715	-18.8566	107.7087	6.6934
69	4.1154	-2.1369	-2.1719	4.4585	-0.1811	5.3034	0.3676	-0.1984	0.8934	1.1385	-0.1472	1.392	-0.7067	0.2693	-0.1717	0.747	-0.0439	0.2739	0.469	-0.1078	0.8198	-14.2865	119.568	32.8382
70	2.6161	0.0014	-3.279	0.1025	-0.3972	5.2729	0.2786	0.6374	1.4067	1.5785	0.1533	1.0808	-0.9365	-0.3422	-0.3745	0.9642	0.0472	0.277	0.5326	0.0512	1.1535	-9.494	129.775	23.8564

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'J' and (resid 96 through 140 )
2	X-RAY DIFFRACTION	2	chain 'J' and (resid 141 through 230 )
3	X-RAY DIFFRACTION	3	chain 'J' and (resid 231 through 281 )
4	X-RAY DIFFRACTION	4	chain 'K' and (resid 2 through 22 )
5	X-RAY DIFFRACTION	5	chain 'K' and (resid 23 through 77 )
6	X-RAY DIFFRACTION	6	chain 'K' and (resid 78 through 178 )
7	X-RAY DIFFRACTION	7	chain 'K' and (resid 179 through 282 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 3 through 57 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 58 through 87 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 88 through 105 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 106 through 178 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 179 through 199 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 200 through 256 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 257 through 282 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 2 through 105 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 106 through 199 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 200 through 281 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 3 through 36 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 37 through 57 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 58 through 87 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 88 through 105 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 106 through 162 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 163 through 178 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 179 through 199 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 200 through 256 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 257 through 282 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 2 through 22 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 23 through 95 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 96 through 140 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 141 through 162 )
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 163 through 199 )
32	X-RAY DIFFRACTION	32	chain 'C' and (resid 200 through 223 )
33	X-RAY DIFFRACTION	33	chain 'C' and (resid 224 through 256 )
34	X-RAY DIFFRACTION	34	chain 'C' and (resid 257 through 280 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 4 through 57 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 58 through 87 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 88 through 178 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 179 through 280 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 4 through 57 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 58 through 105 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 106 through 140 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 141 through 256 )
43	X-RAY DIFFRACTION	43	chain 'E' and (resid 257 through 282 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 3 through 256 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 257 through 282 )
46	X-RAY DIFFRACTION	46	chain 'G' and (resid 2 through 22 )
47	X-RAY DIFFRACTION	47	chain 'G' and (resid 23 through 52 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 53 through 73 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 74 through 140 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 141 through 199 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 200 through 256 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 257 through 282 )
53	X-RAY DIFFRACTION	53	chain 'H' and (resid 3 through 36 )
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 37 through 57 )
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 58 through 87 )
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 88 through 119 )
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 120 through 178 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 179 through 199 )
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 200 through 282 )
60	X-RAY DIFFRACTION	60	chain 'I' and (resid 2 through 22 )
61	X-RAY DIFFRACTION	61	chain 'I' and (resid 23 through 57 )
62	X-RAY DIFFRACTION	62	chain 'I' and (resid 58 through 73 )
63	X-RAY DIFFRACTION	63	chain 'I' and (resid 74 through 105 )
64	X-RAY DIFFRACTION	64	chain 'I' and (resid 106 through 140 )
65	X-RAY DIFFRACTION	65	chain 'I' and (resid 141 through 178 )
66	X-RAY DIFFRACTION	66	chain 'I' and (resid 179 through 199 )
67	X-RAY DIFFRACTION	67	chain 'I' and (resid 200 through 256 )
68	X-RAY DIFFRACTION	68	chain 'I' and (resid 257 through 281 )
69	X-RAY DIFFRACTION	69	chain 'J' and (resid 3 through 65 )
70	X-RAY DIFFRACTION	70	chain 'J' and (resid 66 through 95 )

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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-Protein , 1 types, 12 molecules ABCDEFGHIJKL

-Non-polymers , 8 types, 93 molecules

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Assembly

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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Non-polymers , 8 types, 93 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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