PDB-9r6z: Cubic state of the F420-reducing hydrogenase from Methanothermoco...

ID or keywords:

Entry

Database: PDB / ID: 9r6z

Title

Cubic state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus

Components

(F420-reducing [NiFe]-hydrogenase subunit ...) x 3

Keywords

OXIDOREDUCTASE / [NiFe]-hydrogenase / redox cycle / catalysis / [4Fe-4S]-cluster / F420 cofactor / FAD / hydrogen activation / thermophilic methanogen

Function / homology

FLAVIN-ADENINE DINUCLEOTIDE / Chem-NFU / IRON/SULFUR CLUSTER

Function and homology information

Biological species

Methanothermococcus thermolithotrophicus DSM 2095 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Jespersen, M. / Lemaire, O.N. / Wagner, T.

Funding support

Germany, 3items

Citation

Journal: Chembiochem / Year: 2025
Title: Structural and Spectroscopic Insights into Catalytic Intermediates of a [NiFe]-hydrogenase from Group 3.
Authors: Jespersen, M. / Lorent, C. / Lemaire, O.N. / Zebger, I. / Wagner, T.

History

Deposition	May 13, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release
Revision 1.1	Nov 19, 2025	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9r6z.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb9r6z.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	9r6z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9r6z_validation.pdf.gz	9.3 MB	Display	wwPDB validaton report
Full document	9r6z_full_validation.pdf.gz	9.4 MB	Display
Data in XML	9r6z_validation.xml.gz	140.5 KB	Display
Data in CIF	9r6z_validation.cif.gz	179.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r6/9r6z ftp://data.pdbj.org/pub/pdb/validation_reports/r6/9r6z	HTTPS FTP

-
Related structure data

Related structure data	9r51C 9r52C 9r5iC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: F420-reducing [NiFe]-hydrogenase subunit alpha

B: F420-reducing [NiFe]-hydrogenase subunit beta

C: F420-reducing [NiFe]-hydrogenase subunit gamma

D: F420-reducing [NiFe]-hydrogenase subunit alpha

E: F420-reducing [NiFe]-hydrogenase subunit beta

F: F420-reducing [NiFe]-hydrogenase subunit gamma

G: F420-reducing [NiFe]-hydrogenase subunit alpha

H: F420-reducing [NiFe]-hydrogenase subunit beta

I: F420-reducing [NiFe]-hydrogenase subunit gamma

J: F420-reducing [NiFe]-hydrogenase subunit alpha

K: F420-reducing [NiFe]-hydrogenase subunit beta

L: F420-reducing [NiFe]-hydrogenase subunit gamma

hetero molecules

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

1

A: F420-reducing [NiFe]-hydrogenase subunit alpha

B: F420-reducing [NiFe]-hydrogenase subunit beta

C: F420-reducing [NiFe]-hydrogenase subunit gamma

D: F420-reducing [NiFe]-hydrogenase subunit alpha

E: F420-reducing [NiFe]-hydrogenase subunit beta

F: F420-reducing [NiFe]-hydrogenase subunit gamma

G: F420-reducing [NiFe]-hydrogenase subunit alpha

H: F420-reducing [NiFe]-hydrogenase subunit beta

I: F420-reducing [NiFe]-hydrogenase subunit gamma

J: F420-reducing [NiFe]-hydrogenase subunit alpha

K: F420-reducing [NiFe]-hydrogenase subunit beta

L: F420-reducing [NiFe]-hydrogenase subunit gamma

hetero molecules

A: F420-reducing [NiFe]-hydrogenase subunit alpha

B: F420-reducing [NiFe]-hydrogenase subunit beta

C: F420-reducing [NiFe]-hydrogenase subunit gamma

D: F420-reducing [NiFe]-hydrogenase subunit alpha

E: F420-reducing [NiFe]-hydrogenase subunit beta

F: F420-reducing [NiFe]-hydrogenase subunit gamma

G: F420-reducing [NiFe]-hydrogenase subunit alpha

H: F420-reducing [NiFe]-hydrogenase subunit beta

I: F420-reducing [NiFe]-hydrogenase subunit gamma

J: F420-reducing [NiFe]-hydrogenase subunit alpha

K: F420-reducing [NiFe]-hydrogenase subunit beta

L: F420-reducing [NiFe]-hydrogenase subunit gamma

hetero molecules

A: F420-reducing [NiFe]-hydrogenase subunit alpha

B: F420-reducing [NiFe]-hydrogenase subunit beta

C: F420-reducing [NiFe]-hydrogenase subunit gamma

D: F420-reducing [NiFe]-hydrogenase subunit alpha

E: F420-reducing [NiFe]-hydrogenase subunit beta

F: F420-reducing [NiFe]-hydrogenase subunit gamma

G: F420-reducing [NiFe]-hydrogenase subunit alpha

H: F420-reducing [NiFe]-hydrogenase subunit beta

I: F420-reducing [NiFe]-hydrogenase subunit gamma

J: F420-reducing [NiFe]-hydrogenase subunit alpha

K: F420-reducing [NiFe]-hydrogenase subunit beta

L: F420-reducing [NiFe]-hydrogenase subunit gamma

hetero molecules

defined by author&software
Evidence: native gel electrophoresis, gel filtration
1.27 MDa, 36 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	282.072, 282.072, 282.072
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

-
F420-reducing [NiFe]-hydrogenase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein	F420-reducing [NiFe]-hydrogenase subunit alpha Mass: 45839.492 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: The C-terminal extension has been cleaved off during maturation. Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: coenzyme F420 hydrogenase
#2: Protein	F420-reducing [NiFe]-hydrogenase subunit beta Mass: 31091.084 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: DSM 2095 / Tissue: / / References: coenzyme F420 hydrogenase
#3: Protein	F420-reducing [NiFe]-hydrogenase subunit gamma Mass: 26070.508 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: DSM 2095 / Tissue: / / References: coenzyme F420 hydrogenase

-
Non-polymers , 6 types, 129 molecules

#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER Mass: 195.591 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃HFeN₂NiO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.66 Å³/Da / Density % sol: 73.61 % / Description: Black hexagones
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: The enzyme used for crystallisation was concentrated at 16 mg/ml in a buffer containing 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, 2 mM dithiothreitol and 2 mM FAD. Crystals were obtained ...Details: The enzyme used for crystallisation was concentrated at 16 mg/ml in a buffer containing 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, 2 mM dithiothreitol and 2 mM FAD. Crystals were obtained anaerobically in a Coy tent filled with a N2/H2 (97:3 %) atmosphere by initial screening at 20 degree Celsius using the sitting-drop method on 96-well MRC two-drop crystallisation plates in polystyrene (SWISSCI) containing 90 ul of crystallisation solution in the reservoir. The crystallisation solution was 1.5 M LiSO4 and 100 mM HEPES pH 7.5. Prior to freezing, the crystal was soaked in the crystallisation solution supplemented with 30% (v/v) glycerol.

Crystal

Density Matthews: 4.66 Å³/Da / Density % sol: 73.61 % / Description: Black hexagones

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The enzyme used for crystallisation was concentrated at 16 mg/ml in a buffer containing 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, 2 mM dithiothreitol and 2 mM FAD. Crystals were obtained ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.3871 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3871 Å / Relative weight: 1
Reflection	Resolution: 2.85→49.1 Å / Num. obs: 173025 / % possible obs: 100 % / Redundancy: 7.6 % / CC_1/2: 0.988 / R_merge(I) obs: 0.217 / R_pim(I) all: 0.085 / R_rim(I) all: 0.233 / Net I/σ(I): 6
Reflection shell	Resolution: 2.85→3 Å / Redundancy: 7.8 % / R_merge(I) obs: 1.497 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 25112 / CC_1/2: 0.433 / R_pim(I) all: 0.572 / R_rim(I) all: 1.605 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
BUSTER		refinement
PDB_EXTRACT		data extraction
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.85→31.34 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.37 / Stereochemistry target values: ML
Details: Model was improved in Coot and refined initially with Buster, then Phenix. In Phenix the model was initially refined with hydrogens in riding position and translation libration screw (TLS). ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2101	8753	5.07 %	Random selection
R_work	0.1823	-	-	-
obs	0.1837	172727	99.91 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 82 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→31.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28188	0	562	70	28820

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	29339
X-RAY DIFFRACTION	f_angle_d	0.878	39841
X-RAY DIFFRACTION	f_dihedral_angle_d	16.034	10888
X-RAY DIFFRACTION	f_chiral_restr	0.056	4554
X-RAY DIFFRACTION	f_plane_restr	0.005	4986

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 (%)
2.85-2.88	0.3384	281	0.3169	5394	X-RAY DIFFRACTION	100
2.88-2.92	0.3452	315	0.3123	5387	X-RAY DIFFRACTION	100
2.92-2.95	0.3546	297	0.3131	5374	X-RAY DIFFRACTION	100
2.95-2.99	0.3703	283	0.3096	5508	X-RAY DIFFRACTION	100
2.99-3.03	0.3376	241	0.3035	5463	X-RAY DIFFRACTION	100
3.03-3.07	0.3347	314	0.2804	5363	X-RAY DIFFRACTION	100
3.07-3.11	0.3108	309	0.2701	5417	X-RAY DIFFRACTION	100
3.11-3.16	0.3175	282	0.2634	5452	X-RAY DIFFRACTION	100
3.16-3.21	0.3306	289	0.2633	5448	X-RAY DIFFRACTION	100
3.21-3.26	0.3061	308	0.2637	5402	X-RAY DIFFRACTION	100
3.26-3.32	0.2958	327	0.2512	5474	X-RAY DIFFRACTION	100
3.32-3.38	0.3015	299	0.2342	5361	X-RAY DIFFRACTION	100
3.38-3.44	0.2486	284	0.2231	5452	X-RAY DIFFRACTION	100
3.44-3.51	0.244	284	0.2038	5479	X-RAY DIFFRACTION	100
3.51-3.59	0.2589	293	0.201	5441	X-RAY DIFFRACTION	100
3.59-3.67	0.2399	276	0.1942	5478	X-RAY DIFFRACTION	100
3.67-3.76	0.217	271	0.19	5467	X-RAY DIFFRACTION	100
3.77-3.87	0.2236	258	0.1841	5496	X-RAY DIFFRACTION	100
3.87-3.98	0.2192	296	0.1777	5417	X-RAY DIFFRACTION	100
3.98-4.11	0.2199	282	0.1699	5515	X-RAY DIFFRACTION	100
4.11-4.25	0.1922	282	0.1597	5456	X-RAY DIFFRACTION	100
4.26-4.42	0.1716	303	0.1554	5479	X-RAY DIFFRACTION	100
4.43-4.62	0.1635	325	0.1462	5427	X-RAY DIFFRACTION	100
4.63-4.87	0.1665	274	0.1449	5530	X-RAY DIFFRACTION	100
4.87-5.17	0.1681	289	0.1521	5486	X-RAY DIFFRACTION	100
5.17-5.57	0.1665	296	0.158	5494	X-RAY DIFFRACTION	100
5.57-6.13	0.1794	291	0.1623	5541	X-RAY DIFFRACTION	100
6.13-7	0.1766	290	0.1578	5521	X-RAY DIFFRACTION	100
7.01-8.79	0.1486	303	0.1355	5546	X-RAY DIFFRACTION	100
8.79-31.34	0.1497	311	0.1434	5706	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	2.741	0.1498	-1.024	0.9323	1.8137	4.149	0.6736	-0.2578	-0.4422	0.2567	0.4615	1.3442	0.2618	-0.623	-1.1637	1.1553	-0.5354	-0.0047	1.0098	0.3258	1.2989	-108.8788	35.5135	72.1227
2	1.7599	-0.6024	0.0907	1.7867	-0.0687	1.6342	-0.0229	-0.2797	0.0914	0.1865	-0.0365	0.2818	0.2123	-0.2758	0.0499	0.5339	-0.2488	0.0842	0.6928	0.1021	0.7834	-105.4081	64.1689	67.7813
3	8.8456	0.9397	-1.5817	1.0077	0.5907	0.8912	0.2432	-1.5437	-0.3151	0.6678	-0.2451	0.2953	0.1332	0.0418	0.0404	1.0882	-0.3121	0.2109	1.0514	0.2181	1.0091	-104.1193	44.9266	85.4807
4	0.9818	-0.5289	-0.1822	1.3762	-0.0599	1.4327	0.0381	-0.1633	-0.0791	0.0891	-0.1535	0.1085	0.2617	-0.0849	0.1273	0.6067	-0.2184	0.0717	0.6982	0.1493	0.8583	-93.2118	56.9783	67.8595
5	0.8006	0.2714	-0.4392	2.1262	0.2024	0.7297	-0.2581	-0.277	-0.7395	-0.024	0.0608	0.4446	0.8546	-0.732	0.2212	0.8927	-0.3958	0.0793	1.0153	0.2874	1.133	-106.0036	43.8305	73.686
6	0.9701	-1.0067	-0.937	1.8507	-0.4283	4.6871	0.1215	0.0194	0.2366	-0.0492	0.057	0.3338	-0.4816	-0.3402	-0.1715	0.4244	-0.0591	-0.0412	0.6873	-0.0474	0.8509	-120.2725	95.425	47.2535
7	0.926	0.1798	-0.3836	1.2237	-0.448	1.1437	0.0314	0.0039	0.0141	-0.095	-0.0113	0.5745	-0.0855	-0.5846	-0.0177	0.4318	-0.0463	-0.1067	0.9295	0.044	0.9852	-124.1645	89.383	38.8855
8	2.3463	1.6752	-0.4041	2.8096	-2.4046	3.2226	0.3104	-0.2935	-0.3239	0.4063	-0.3616	0.6494	0.0746	-0.1392	0.0572	0.7635	-0.3682	0.1493	0.9136	0.0753	1.179	-120.5302	47.5011	66.0313
9	2.0637	-0.8242	0.0616	0.6654	0.2716	1.1464	0.1824	0.0151	-0.5302	-0.1008	-0.096	0.8278	0.3308	-0.4517	-0.0808	0.7099	-0.3652	-0.0027	0.8448	0.1111	1.1006	-119.2504	51.1962	50.9948
10	1.0854	-1.4301	1.105	2.3349	-0.903	4.0771	-0.0582	0.0829	-0.0883	0.0101	-0.284	0.1627	0.1868	-0.0939	0.3571	0.4818	-0.2353	-0.0568	0.7674	0.0033	1.0573	-116.2237	70.3935	40.5233
11	3.3101	1.6082	-1.1874	4.1185	0.6558	1.9176	0.2806	0.3934	-0.3909	-0.6567	0.3052	0.8594	0.1704	-0.5142	-0.6019	0.5886	-0.0986	-0.3505	0.964	0.0049	0.7188	-108.2544	85.6167	-1.2385
12	0.8981	-0.0414	-0.1839	1.5528	0.1264	1.2225	0.0147	0.2257	-0.2117	-0.0297	-0.0179	0.0355	0.2641	-0.0448	0.0016	0.5697	-0.1227	-0.2159	0.5325	0.0083	0.5717	-87.7635	66.897	11.2525
13	3.9092	1.3023	3.1217	6.5831	4.1496	6.9518	0.1826	0.4819	-0.055	-0.7338	0.1913	-0.3828	-0.3101	-0.0017	-0.3521	0.7505	-0.0089	-0.1324	0.6811	0.0716	0.5211	-93.4573	85.297	-8.3409
14	3.5755	-0.6345	-1.6589	3.4558	0.7499	0.9512	-0.0709	0.0086	0.3863	-0.039	0.1528	0.0358	0.0797	-0.2722	-0.0812	0.5853	-0.0339	-0.2076	0.6079	0.0613	0.4759	-93.2581	88.3497	15.7765
15	1.502	-0.3638	-0.4313	2.4031	0.0006	0.3928	0.0383	0.1078	-0.0379	0.0474	-0.0684	-0.1385	-0.0226	-0.0169	0.0388	0.5356	-0.1067	-0.1973	0.5094	0.043	0.4714	-83.5675	77.9952	13.5121
16	2.8335	-0.4644	1.6793	1.9787	-1.2318	5.8695	0.1254	0.3384	0.0341	-0.2083	0.1232	0.584	0.2416	-0.7078	-0.2276	0.4368	-0.0888	-0.1504	0.5066	-0.035	0.5267	-97.6424	81.9855	10.6287
17	2.5626	1.3123	1.0053	2.3249	-0.1863	4.2523	-0.1436	0.0661	-0.8771	0.3672	0.0007	0.4014	0.9459	-0.2642	0.1476	1.1462	-0.0428	-0.0194	0.5542	-0.1069	1.2221	-86.0584	22.5049	26.0558
18	1.3379	-0.6668	-1.4325	1.3713	-0.4917	3.707	0.1443	-0.1615	-0.3348	0.1476	-0.0193	-0.0039	0.1329	0.2475	-0.1579	0.7341	-0.1577	-0.1448	0.5702	0.0241	0.9128	-80.3278	36.905	29.7964
19	1.8212	-1.5852	-0.3032	1.64	-0.2166	1.2193	-0.0247	-0.0857	0.1544	-0.4704	-0.0947	-0.2621	-0.1582	0.2648	0.2264	0.8465	-0.1738	-0.1741	0.498	-0.037	0.8562	-85.6083	47.3306	21.8077
20	3.36	-1.6961	-1.2763	3.1507	-1.0133	1.6845	0.2175	0.2057	-1.0322	-0.2688	-0.0351	0.5071	-0.03	0.1667	-0.1604	0.881	-0.3154	-0.1123	0.5643	-0.1034	0.9579	-95.431	38.3296	23.5625
21	1.6737	-0.1017	0.6073	1.2616	1.198	1.7447	0.0764	0.1924	-0.6158	-0.3602	-0.0295	0.4805	0.558	-0.0503	-0.1045	1.0524	-0.2135	-0.2446	0.5405	-0.0256	0.9745	-93.8323	39.5303	24.1979
22	5.7169	-1.634	-0.2755	0.5123	0.265	2.5862	0.1729	-0.2569	-0.6738	0.3713	-0.0823	-0.0202	0.6426	-0.3631	-0.1165	1.0703	-0.218	-0.131	0.4929	0.1298	0.9195	-85.5349	32.5082	49.51
23	6.8706	-0.4124	-1.2511	1.474	0.0625	1.8074	-0.442	-0.2611	-1.0344	0.0711	0.406	-0.0271	0.5917	-0.2259	-0.005	1.3306	0.0047	0.0098	0.5917	0	1.1783	-83.1568	23.702	48.6681
24	1.8543	-0.5457	-2.0011	0.1893	0.6518	2.347	-0.0311	-0.2245	-1.0439	-0.5333	0.2537	1.2807	0.8993	0.0564	-0.1028	1.2129	-0.4709	-0.0515	0.7132	0.0739	1.2834	-99.5344	30.9364	45.8969
25	3.653	0.428	-0.0905	1.4334	0.2374	0.3474	-0.0401	0.1077	-0.884	-0.0515	-0.1218	0.3465	0.6826	-0.1053	0.1692	1.1858	-0.2091	-0.1801	0.5564	-0.1207	1.182	-90.2507	24.932	22.6967
26	7.4407	4.0195	-2.793	2.3379	-2.3096	5.1306	0.1429	0.2367	-1.2726	0.5906	0.3068	-0.122	1.417	-0.066	-0.4065	1.5106	-0.0003	0.0025	0.7403	-0.1494	1.2663	-84.9664	13.9408	23.6145
27	2.003	-2.5136	-0.0745	3.3324	-0.3641	0.7658	0.2942	-0.4076	-0.4732	-0.2236	0.1023	0.3205	0.3676	-0.2988	-0.3531	1.2438	-0.4868	-0.1851	0.865	-0.0441	1.2555	-109.0969	28.4798	34.9074
28	3.3102	-0.5195	1.9574	2.5754	-2.2025	3.3374	-0.1467	0.5767	0.0269	-0.3577	-0.2142	0.4719	-0.1321	-0.0114	0.3373	0.7233	-0.1767	-0.3098	0.8464	-0.1084	0.7502	-108.3627	66.6895	0.9413
29	1.6269	-0.8005	-0.34	3.7698	1.2179	1.3911	0.1246	0.1537	-0.3373	-0.2096	-0.0558	0.6065	0.2679	-0.3853	-0.035	0.6062	-0.2212	-0.24	0.7886	0.0067	0.7737	-112.4375	61.5569	15.13
30	2.9727	-0.6517	-1.4782	3.234	-2.8632	4.1736	-0.0189	0.0576	-0.3229	0.2859	-0.2275	0.1593	-0.2162	0.096	0.2628	0.5662	-0.1923	-0.1952	0.5824	-0.0199	0.9115	-102.102	48.967	30.0295
31	2.7884	-1.3756	0.4363	4.7456	-1.0904	3.8123	-0.1242	0.7753	-0.4082	-0.6553	0.0614	-0.4109	0.0111	1.0439	-0.0129	0.591	0.1835	0.2891	1.0547	-0.1026	0.7063	11.9174	63.8635	19.5788
32	4.6335	-1.0742	1.2394	1.8665	0.2809	1.5588	-0.2993	-0.1856	-0.9727	-0.3736	0.1239	0.1184	-0.2786	0.087	0.2164	0.5804	0.1562	0.1198	0.7111	0.0333	0.4926	-6.4123	71.49	17.5368
33	1.3269	-0.0321	0.3924	1.309	0.1424	1.2906	0.0736	-0.0187	-0.2568	-0.1065	-0.0944	0.0869	0.272	0.1844	0.0171	0.5053	0.1723	0.0898	0.5463	-0.081	0.4975	-16.1499	51.4226	26.8307
34	3.8891	-1.0386	-0.6885	8.8117	3.2235	4.1878	0.1576	0.243	-0.2556	0.1325	-0.2758	-0.983	0.5146	0.7096	0.0925	0.4774	0.1956	0.0699	0.7801	-0.0003	0.7083	10.2155	56.1417	34.4502
35	0.869	0.8629	0.6681	1.943	0.1268	1.0788	0.0745	-0.073	0.1446	-0.0516	-0.1042	0.0089	0.0777	0.1135	0.0353	0.43	0.142	0.1259	0.5743	-0.0346	0.4875	-11.8937	65.4003	32.9243
36	3.9673	-1.1215	1.0391	3.1357	0.2105	1.4454	-0.008	0.6323	-0.0715	-0.2832	-0.0836	-0.3833	0.0084	0.4786	0.071	0.495	0.1265	0.1629	0.6291	-0.0187	0.4186	-3.1836	66.8094	24.8197
37	4.8991	0.0898	-0.4363	2.9034	2.3043	3.6892	-0.2708	0.9485	-1.2329	-0.1769	0.1478	-0.2622	0.0597	0.3781	0.0186	1.0481	0.128	-0.093	0.5744	-0.294	0.966	-42.0313	28.2119	-5.6019
38	5.6148	0.7555	0.9251	2.3521	0.3682	2.5176	-0.1122	-0.1896	-1.1397	0.1873	0.0893	0.1717	0.618	-0.1951	-0.0273	0.9193	0.0416	0.0179	0.4895	-0.0683	0.6867	-47.998	34.4637	12.6745
39	1.8274	-0.917	1.9449	5.0652	-1.9059	2.3323	-0.1243	-0.3345	0.1386	0.3203	0.1205	0.2833	-0.2002	-0.554	0.0369	0.7353	0.0237	0.0378	0.53	-0.07	0.6051	-49.7555	46.4582	11.3269
40	2.7162	0.1274	-0.4443	0.2414	0.1404	2.9456	-0.0155	0.2716	-0.1783	-0.217	-0.0238	0.2561	0.3186	0.0344	0.0271	0.8037	0.1388	0.0053	0.4722	-0.1435	0.6057	-34.0467	43.9504	8.4115
41	3.4805	-1.2781	-0.5119	0.787	-0.2541	0.6779	-0.1131	0.1592	-0.2471	-0.1636	0.0299	0.0625	0.2052	-0.0681	0.0535	0.7911	0.0967	-0.0816	0.4766	-0.197	0.5986	-44.8358	47.8859	2.329
42	5.3015	-0.2343	-1.3271	5.7969	1.107	2.0771	-0.2761	0.6991	-0.9385	-0.4383	0.264	0.7193	0.5551	0.0173	-0.1133	0.7698	-0.0868	-0.1738	0.6297	-0.1177	0.8031	-63.6345	45.87	-0.658
43	1.3252	-0.1454	-1.6256	3.6107	0.8566	2.1199	0.3424	0.6097	-0.4681	-0.8826	-0.2168	-0.1256	0.3636	-0.1937	-0.1739	1.0817	0.1339	-0.1106	0.6972	-0.1997	0.5845	-44.6977	46.0949	-8.2657
44	3.5899	1.3999	1.3058	1.1608	-0.1969	1.9379	-0.0763	0.2422	-0.8752	-0.035	0.2366	0.2713	0.2569	-0.0434	-0.1299	1.021	0.0411	-0.0816	0.5189	-0.2141	0.9183	-43.7877	27.71	2.6768
45	3.2832	-0.756	3.8926	0.7785	-1.2163	4.7412	0.1827	0.5953	-0.795	-0.084	0.2016	-0.4242	0.0506	0.3109	-0.4863	1.2213	0.0667	-0.1157	0.698	-0.2052	1.1122	-51.355	22.0395	-1.0468
46	3.2281	1.9818	-1.2443	3.5508	-2.2016	2.017	-0.0724	1.0848	-0.4624	-0.9379	0.1938	0.01	0.4586	-0.2214	-0.105	1.0757	0.2103	-0.1328	0.77	-0.2594	0.662	-40.5548	45.5695	-16.8845
47	6.3883	-0.9577	-0.2305	0.2471	0.3956	1.2785	-0.1554	0.1357	-0.5426	-0.5098	0.0669	-0.3277	0.1725	0.4728	0.0805	0.7396	0.2404	0.228	0.8568	-0.0424	0.7078	1.7921	52.293	10.5759
48	1.1793	1.5081	0.7884	5.0242	-0.4128	1.2936	-0.0073	0.3533	-0.2431	-0.3708	0.1582	-0.494	0.0192	0.4068	-0.1482	0.6481	0.172	0.185	0.8068	-0.0859	0.5767	-7.6407	59.9056	2.6845
49	5.1454	0.979	1.0595	0.5859	-0.1648	2.9693	-0.1995	0.3389	-0.094	-0.2326	0.0301	-0.1093	0.3606	0.1137	0.1774	0.6906	0.097	0.0745	0.5095	-0.1082	0.4381	-28.4302	54.655	-1.0877
50	4.1409	2.6801	-2.0518	6.9584	1.2169	2.2504	-0.4044	0.8371	0.0512	-0.7836	0.2975	0.6401	-0.062	-0.0637	0.0792	1.025	0.1067	-0.1859	0.9356	-0.0383	0.4403	-64.6692	74.5343	-22.3258
51	1.9214	0.051	-0.3956	2.1548	-0.1129	0.1002	0.1061	0.0306	0.0042	-0.2905	-0.2068	-0.1407	0.0265	0.1182	0.0931	0.5725	0.0421	-0.0565	0.594	0.0553	0.2771	-49.79	83.397	0.3295
52	3.7645	0.8352	2.4715	2.5299	-1.0059	9.2196	-0.055	0.9078	0.3463	-0.6125	-0.0297	-0.0714	-0.3529	0.7624	0.0815	0.8606	0.0652	0.054	0.6375	0.102	0.3578	-50.4732	98.4346	-16.0631
53	1.6878	0.4969	0.2984	0.9779	1.1787	1.6953	0.0229	0.2248	0.3943	-0.5364	-0.0706	-0.096	-0.2314	0.1308	0.0153	0.6937	0.0032	0.0064	0.6	0.0951	0.3079	-48.9836	100.842	-4.0036
54	5.2511	1.6336	-3.1055	4.0111	-2.235	2.3332	0.3475	1.3232	0.3108	-0.7133	0.389	0.7534	-0.7014	-1.1815	-0.7427	0.9146	0.0317	-0.2186	0.813	0.0204	0.6131	-72.6189	88.5841	-17.5276
55	1.9367	0.2417	-0.0382	2.2955	-0.0081	0.7706	0.1085	-0.0371	-0.1137	-0.2904	-0.0781	0.134	0.0338	-0.0344	-0.0343	0.5221	0.0446	-0.0477	0.5046	0.0458	0.2614	-59.0727	83.6462	2.3854
56	5.1359	-0.0815	1.7156	3.3644	0.8009	1.4786	0.3267	0.83	-0.687	-0.454	0.1674	0.0044	0.106	0.1167	-0.4454	0.8262	0.1346	-0.0834	0.7382	-0.0537	0.4048	-63.2655	80.8789	-16.2153
57	2.7701	-0.5581	0.5982	1.799	-0.3085	2.3012	-0.0543	0.2464	0.515	-0.261	0.0862	-0.4998	-0.549	0.3326	-0.0464	0.7773	-0.1	0.2904	0.6614	0.0455	0.6304	-12.6472	105.4335	3.4936
58	1.2612	0.1832	0.258	1.0791	-0.2393	1.8028	-0.0105	0.4732	0.2677	-0.3103	-0.0142	-0.3657	-0.2488	0.507	0.0201	0.6833	-0.0367	0.2799	0.8263	0.1104	0.5998	-7.4369	96.6579	-0.633
59	3.5324	-0.3568	0.979	0.5703	0.1976	3.364	-0.2617	0.562	-0.2736	-0.8938	-0.0514	-0.1477	-0.191	0.0819	0.3473	1.2178	0.0857	-0.0272	0.9175	0.044	0.3952	-48.8911	82.2792	-24.7412
60	2.9002	1.2342	-0.8141	3.616	-1.1211	1.4411	-0.0997	0.6108	-0.3156	-0.632	0.0371	-0.1618	0.1704	0.2718	0.0175	0.89	0.1227	0.0404	0.8422	-0.0245	0.3456	-36.7288	75.1462	-18.1993
61	5.833	-0.3322	0.7432	2.7346	1.868	1.5339	0.0991	-0.0051	-0.1714	-0.3369	0.0877	-0.1243	-0.1394	0.2278	-0.1759	0.6412	0.0702	0.1312	0.67	0.0515	0.3353	-21.4713	81.7649	-3.6717

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 194 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 195 through 216 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 217 through 368 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 369 through 393 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 80 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 81 through 282 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 2 through 60 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 61 through 170 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 171 through 241 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 33 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 34 through 195 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 196 through 215 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 216 through 249 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 250 through 343 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 344 through 393 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 1 through 28 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 29 through 80 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 81 through 96 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 97 through 114 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 115 through 139 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 140 through 164 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 165 through 181 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 182 through 194 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 195 through 236 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 237 through 251 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 252 through 282 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 2 through 60 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 61 through 170 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 171 through 241 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 2 through 28 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 29 through 51 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 52 through 195 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 196 through 215 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 216 through 343 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 344 through 393 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 1 through 15 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 16 through 51 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 52 through 80 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 81 through 114 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 115 through 154 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 155 through 184 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 185 through 205 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 206 through 236 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 237 through 251 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 252 through 282 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 2 through 60 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 61 through 156 )
49	X-RAY DIFFRACTION	49	chain 'I' and (resid 157 through 241 )
50	X-RAY DIFFRACTION	50	chain 'J' and (resid 2 through 28 )
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 29 through 112 )
52	X-RAY DIFFRACTION	52	chain 'J' and (resid 113 through 145 )
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 146 through 195 )
54	X-RAY DIFFRACTION	54	chain 'J' and (resid 196 through 215 )
55	X-RAY DIFFRACTION	55	chain 'J' and (resid 216 through 368 )
56	X-RAY DIFFRACTION	56	chain 'J' and (resid 369 through 393 )
57	X-RAY DIFFRACTION	57	chain 'K' and (resid 1 through 80 )
58	X-RAY DIFFRACTION	58	chain 'K' and (resid 81 through 282 )
59	X-RAY DIFFRACTION	59	chain 'L' and (resid 2 through 60 )
60	X-RAY DIFFRACTION	60	chain 'L' and (resid 61 through 170 )
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 171 through 241 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
F420-reducing [NiFe]-hydrogenase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL

-
Non-polymers , 6 types, 129 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-F420-reducing [NiFe]-hydrogenase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL

-Non-polymers , 6 types, 129 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
F420-reducing [NiFe]-hydrogenase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL

-
Non-polymers , 6 types, 129 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi