PDB-6rjr: Crystal structure of a Fungal Catalase at 1.9 Angstrom

ID or keywords:

Entry

Database: PDB / ID: 6rjr

Title

Crystal structure of a Fungal Catalase at 1.9 Angstrom

Components

Catalase

Keywords

OXIDOREDUCTASE / Kluyveromyces lactis / Catalase / Heme / NADP

Function / homology

Function and homology information

catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / nucleotide binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function

Biological species

Kluyveromyces lactis (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.895 Å

Authors

Gomez, S. / Navas-Yuste, S. / Payne, A.M. / Rivera, W. / Lopez-Estepa, M. / Brangbour, C. / Fulla, D. / Juanhuix, J. / Fernandez, F.J. / Vega, M.C.

Funding support

Spain, 3items

Organization	Grant number	Country
Spanish Ministry of Economy and Competitiveness	CTQ2015-66206-C2-2-R	Spain
Spanish Ministry of Economy and Competitiveness	SAF2015-72961-EXP	Spain
Spanish National Research Council	PIE-20160E064	Spain

Citation

Journal: Free Radic. Biol. Med. / Year: 2019
Title: Peroxisomal catalases from the yeasts Pichia pastoris and Kluyveromyces lactis as models for oxidative damage in higher eukaryotes.
Authors: Gomez, S. / Navas-Yuste, S. / Payne, A.M. / Rivera, W. / Lopez-Estepa, M. / Brangbour, C. / Fulla, D. / Juanhuix, J. / Fernandez, F.J. / Vega, M.C.

History

Deposition	Apr 29, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 11, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	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_conn_angle / struct_conn Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6rjr.cif.gz	855.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6rjr.ent.gz	708.9 KB	Display	PDB format
PDBx/mmJSON format	6rjr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6rjr_validation.pdf.gz	3.4 MB	Display	wwPDB validaton report
Full document	6rjr_full_validation.pdf.gz	3.5 MB	Display
Data in XML	6rjr_validation.xml.gz	85 KB	Display
Data in CIF	6rjr_validation.cif.gz	121.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rj/6rjr ftp://data.pdbj.org/pub/pdb/validation_reports/rj/6rjr	HTTPS FTP

-
Related structure data

Related structure data	6rjnSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xq1-3 2xq1-2 1f4j-d 2xq1-4 5gkn-d 6pt7-1 2xq1-1 1a4e-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#57 - Sep 2004 Catalase similarity (16) #34 - Oct 2002 Dihydrofolate Reductase similarity (1)

Deposited unit

A: Catalase

B: Catalase

C: Catalase

D: Catalase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	96.670, 131.620, 176.670
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Catalase Mass: 61077.281 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The amino acid sequence of the N-terminal purification tag is: MKHHHHHHPMSDYDIPTTENLYFQGA. Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: KLLA0_D11660g / Plasmid: pETM-11 Details (production host): N-terminal hexahistidine tag, cleavable with TEV protease Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6CR58, catalase

#1: Protein

Catalase

Mass: 61077.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The amino acid sequence of the N-terminal purification tag is: MKHHHHHHPMSDYDIPTTENLYFQGA.
Source: (gene. exp.)

Kluyveromyces lactis (yeast) / Gene: KLLA0_D11660g / Plasmid: pETM-11
Details (production host): N-terminal hexahistidine tag, cleavable with TEV protease
Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6CR58, catalase

-
Non-polymers , 6 types, 1278 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1253 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.7 % / Description: Very elongated, thin prisms and needles.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M sodium citrate, pH 5.5, 20% (w/v) polyethylene glycol (PEG) 3000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97922 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2016 / Details: KIRKPATRICK-BAEZ (KB) FOCUSING SYSTEM
Radiation	Monochromator: SI(111) CHANNEL-CUT MONOCHROMATOR, CRYOCOOLED Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97922 Å / Relative weight: 1
Reflection	Resolution: 1.895→46.98 Å / Num. obs: 764478 / % possible obs: 98.92 % / Redundancy: 4.3 % / B_iso Wilson estimate: 21.39 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.1358 / R_pim(I) all: 0.0742 / R_rim(I) all: 0.1554 / Net I/σ(I): 8.68
Reflection shell	Resolution: 1.895→1.963 Å / Redundancy: 4 % / R_merge(I) obs: 0.5339 / Num. unique obs: 63907 / CC_1/2: 0.238 / R_pim(I) all: 0.2999 / R_rim(I) all: 0.6153 / % possible all: 91.62

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS	Oct 15, 2015	data reduction
Aimless	0.5.17	data scaling
PHASER	2.6.0	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: wwPDB 6RJN

6rjn

Resolution: 1.895→46.98 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.22

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2413	8833	5 %	RANDOM SELECTION
R_work	0.1809	-	-	-
obs	0.1839	176645	98.93 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.895→46.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16094	0	436	1253	17783

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	17086
X-RAY DIFFRACTION	f_angle_d	1.21	23294
X-RAY DIFFRACTION	f_dihedral_angle_d	14.218	10130
X-RAY DIFFRACTION	f_chiral_restr	0.061	2372
X-RAY DIFFRACTION	f_plane_restr	0.008	3068

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 (%)
1.8954-1.9169	0.3945	225	0.3851	4274	X-RAY DIFFRACTION	77
1.9169-1.9395	0.4206	290	0.3658	5508	X-RAY DIFFRACTION	98
1.9395-1.9631	0.3688	294	0.3438	5581	X-RAY DIFFRACTION	100
1.9631-1.988	0.3996	295	0.3224	5611	X-RAY DIFFRACTION	100
1.988-2.0141	0.369	295	0.314	5603	X-RAY DIFFRACTION	100
2.0141-2.0417	0.3532	293	0.3107	5569	X-RAY DIFFRACTION	100
2.0417-2.0709	0.351	294	0.3018	5587	X-RAY DIFFRACTION	100
2.0709-2.1018	0.3319	295	0.2823	5601	X-RAY DIFFRACTION	100
2.1018-2.1347	0.3246	294	0.2731	5590	X-RAY DIFFRACTION	100
2.1347-2.1697	0.3526	296	0.2732	5621	X-RAY DIFFRACTION	100
2.1697-2.2071	0.3214	297	0.265	5640	X-RAY DIFFRACTION	100
2.2071-2.2472	0.3261	294	0.2657	5584	X-RAY DIFFRACTION	100
2.2472-2.2904	0.3101	292	0.2484	5558	X-RAY DIFFRACTION	99
2.2904-2.3372	0.2805	295	0.2276	5594	X-RAY DIFFRACTION	100
2.3372-2.388	0.3176	296	0.222	5626	X-RAY DIFFRACTION	100
2.388-2.4435	0.2765	296	0.2016	5625	X-RAY DIFFRACTION	100
2.4435-2.5046	0.2597	295	0.1965	5615	X-RAY DIFFRACTION	100
2.5046-2.5724	0.2831	297	0.188	5631	X-RAY DIFFRACTION	100
2.5724-2.6481	0.2692	296	0.1858	5637	X-RAY DIFFRACTION	100
2.6481-2.7335	0.26	298	0.1761	5646	X-RAY DIFFRACTION	100
2.7335-2.8312	0.2721	294	0.1735	5597	X-RAY DIFFRACTION	99
2.8312-2.9445	0.2179	298	0.1578	5651	X-RAY DIFFRACTION	100
2.9445-3.0785	0.2231	297	0.1455	5654	X-RAY DIFFRACTION	100
3.0785-3.2408	0.2097	298	0.1399	5666	X-RAY DIFFRACTION	100
3.2408-3.4438	0.1955	299	0.1379	5682	X-RAY DIFFRACTION	100
3.4438-3.7096	0.187	299	0.1163	5665	X-RAY DIFFRACTION	99
3.7096-4.0827	0.1488	300	0.1024	5710	X-RAY DIFFRACTION	100
4.0827-4.673	0.1603	301	0.0959	5710	X-RAY DIFFRACTION	99
4.673-5.8857	0.1616	303	0.1094	5767	X-RAY DIFFRACTION	99
5.8857-46.9944	0.1858	317	0.1583	6009	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	1.2688	0.1372	0.3849	0.0343	-0.1024	1.3407	0.0916	-0.3864	-0.0261	0.1738	0.0138	-0.2687	0.2346	0.0328	-0.0878	0.2358	-0.0444	-0.0207	0.3772	-0.0305	0.2204	80.279	59.9102	51.4949
2	0.6985	0.0495	-0.22	1.7059	0.6405	0.9569	0.0295	-0.0518	-0.0484	0.1041	0.0853	-0.0937	0.1066	-0.0433	-0.1154	0.1233	0.0119	-0.0173	0.1509	0.0099	0.1468	76.8593	46.7196	26.1317
3	0.629	0.11	0.3015	0.6283	-0.1615	0.4635	-0.0132	-0.0144	0.0501	-0.0301	-0.0191	0.1194	-0.0253	-0.0684	0.0283	0.1799	-0.0086	-0.0231	0.1701	-0.0254	0.1656	69.2625	51.4402	10.6164
4	1.0027	-0.0079	-0.0376	1.1813	-0.0451	1.6817	0.0207	0.0482	-0.1118	-0.0389	-0.0139	0.155	0.1086	-0.0938	0.006	0.1049	-0.0416	-0.043	0.1643	-0.0154	0.1404	65.5868	43.0977	11.9631
5	0.9157	0.2164	0.0367	0.0168	-0.0229	0.1457	0.0688	-0.0931	-0.0644	0.0184	-0.0508	-0.0003	0.0594	0.0032	-0.0307	0.1999	-0.0028	-0.0103	0.162	-0.0191	0.1589	87.8652	46.3779	22.7575
6	1.1078	0.0937	-0.4329	0.2778	-0.2203	0.7022	-0.0861	0.2785	-0.1313	-0.0057	0.0571	0.1185	0.061	-0.01	0.0109	0.2702	-0.0456	-0.025	0.2522	-0.0783	0.2176	73.5233	45.7843	-2.5865
7	2.4219	-0.5901	-1.3351	4.8945	-0.5727	2.0252	-0.0139	0.2419	0.0948	-0.2399	0.0531	0.3116	-0.0737	-0.3085	-0.0107	0.1519	0.0014	-0.1001	0.2776	-0.0311	0.2167	52.4531	62.3143	-0.6313
8	0.5501	-0.0244	0.0408	0.3772	0.3983	0.6196	-0.0462	0.0563	0.3321	-0.1244	-0.0324	0.0701	-0.2122	-0.0913	0.0429	0.2234	0.0166	-0.059	0.1879	-0.0353	0.376	78.1705	78.5	15.9456
9	0.4259	0.0193	0.1971	0.8667	-0.0926	0.5133	-0.0127	-0.2014	0.2595	0.0557	-0.089	0.2246	-0.0594	-0.2535	0.0812	0.1954	0.0287	0.0101	0.3556	-0.159	0.3993	63.764	73.296	39.163
10	0.1668	0.016	-0.1383	0.5557	0.1175	0.4628	-0.0563	-0.0891	0.3507	-0.0288	-0.0915	0.2294	-0.1197	-0.2331	0.1816	0.2433	0.101	-0.068	0.3357	-0.1889	0.5898	60.6506	86.7603	32.9946
11	1.836	-1.2087	-1.0926	3.9183	-0.0216	2.1467	-0.1651	-0.5192	0.5673	0.5332	-0.0133	0.2126	-0.251	-0.0989	-0.0758	0.274	0.1062	0.0063	0.513	-0.3515	0.5883	62.3442	91.1588	53.8524
12	0.4696	-0.1781	-0.5482	0.7684	0.3759	0.7318	-0.0851	-0.119	0.2755	-0.065	-0.0434	0.1749	-0.1804	-0.0593	0.042	0.2105	0.0462	-0.0738	0.1759	-0.114	0.4523	76.0946	83.9982	32.17
13	1.7272	0.427	0.7577	1.2268	0.8662	2.1556	-0.1319	-0.0248	0.3148	-0.128	0.0597	0.0567	-0.2736	-0.0594	0.0527	0.243	0.0142	-0.0621	0.1304	0.0137	0.3499	95.857	90.8844	29.57
14	1.5622	0.2377	0.1835	0.3303	0.0069	0.1838	0.0245	-0.3497	0.4426	0.1244	-0.1323	0.4105	-0.1301	-0.2575	0.0856	0.2689	0.051	0.0209	0.486	-0.2257	0.5272	64.8493	84.0356	53.3282
15	2.5503	-0.8552	-0.2166	2.0119	-0.1723	1.9683	0.0316	-0.3445	-0.1715	0.178	-0.1691	0.5086	0.1834	-0.4868	0.1032	0.2147	-0.1079	0.127	0.6276	-0.2389	0.5508	47.2729	64.2517	47.0882
16	1.9684	0.1978	0.1624	1.7029	-0.6554	0.5645	0.0047	0.0343	-0.1493	0.1911	-0.0652	-0.0317	0.0534	-0.1057	0.0662	0.2124	-0.0179	-0.0396	0.1706	-0.0432	0.2295	97.9091	43.5964	18.1942
17	0.4243	0.0409	0.3438	0.6603	0.4397	1.5783	0.0532	-0.0859	-0.0638	0.1767	-0.0407	-0.0763	0.2032	-0.2408	-0.029	0.2	-0.0374	0.0053	0.1712	-0.0096	0.1197	101.3669	58.3609	44.7075
18	0.3876	0.2271	0.2164	0.8328	0.0287	0.9399	0.019	-0.0394	0.0817	0.1504	-0.0479	-0.0293	0.0273	0.0022	0.0336	0.176	-0.0025	-0.0348	0.1436	-0.059	0.1831	107.9408	75.7694	46.8405
19	0.8541	0.3092	0.0293	1.2741	0.3619	0.6543	0.0769	-0.2333	0.0064	0.3151	-0.0438	-0.189	0.1506	0.0377	-0.0546	0.231	-0.0121	-0.0853	0.1788	-0.028	0.1787	112.2926	69.3259	55.6689
20	0.689	0.2275	0.2307	1.0412	0.599	0.618	0.0748	-0.1069	0.0173	0.1655	-0.1511	0.0636	0.1352	-0.107	0.0488	0.1812	-0.0253	-0.0101	0.1801	-0.0275	0.1271	97.6011	63.9316	47.1264
21	2.2471	-0.6323	0.5406	1.5491	0.3213	2.2448	0.2019	-0.3091	-0.0567	0.198	-0.0208	0.1965	0.1404	-0.1623	-0.1013	0.2311	-0.0709	0.0151	0.2651	-0.0372	0.1711	78.1583	55.6681	47.3257
22	0.6989	-0.2531	-0.1656	0.5219	0.4313	0.8784	-0.1014	-0.2647	0.0419	0.2085	-0.0936	0.0819	0.0479	-0.1974	0.1348	0.277	-0.0242	-0.0209	0.239	-0.0949	0.3113	103.7309	83.5331	59.5367
23	1.9381	-0.772	-0.8532	2.6277	-0.8065	4.1744	0.0501	0.0651	-0.0662	-0.0988	0.042	-0.3353	-0.0953	0.1688	-0.0757	0.1803	-0.0312	-0.0358	0.1795	-0.0864	0.3727	124.5424	90.5518	43.5708
24	0.8848	-0.1364	-0.6143	1.3375	0.2485	0.641	-0.0952	-0.0132	0.1594	-0.1755	-0.1739	0.0165	-0.1426	-0.2071	0.2368	0.2487	0.0016	-0.0713	0.227	-0.0924	0.4328	91.9331	90.9088	37.3263
25	1.0487	0.0098	-0.1865	0.5373	0.0476	0.7087	-0.0552	0.1042	0.2038	-0.0684	0.076	-0.041	-0.0969	0.009	-0.0082	0.1778	-0.0165	-0.023	0.1384	0.0027	0.1833	105.4908	75.3664	13.2282
26	1.2595	-0.0223	0.2293	0.5729	-0.3307	0.8075	-0.0195	0.0342	-0.1081	-0.014	0.0482	-0.1296	-0.0055	0.1432	-0.0051	0.1471	-0.0007	0.0064	0.1649	-0.0622	0.1344	112.862	55.8446	15.2004
27	1.4868	0.0384	0.3314	0.8884	0.1505	1.0455	0.0067	0.338	0.2455	-0.1691	0.0212	-0.1869	-0.0686	0.1229	0.0101	0.195	-0.0373	0.0299	0.228	-0.0031	0.136	114.8336	68.6696	1.7697
28	0.5516	-0.4453	0.0311	1.0454	-0.0988	0.5563	-0.044	0.0679	0.2347	-0.0136	0.0357	-0.2095	-0.1877	0.1575	0.0275	0.212	-0.0727	0.0173	0.2229	0.0005	0.2976	119.7606	76.968	14.065
29	2.6484	-0.0908	-1.6994	5.9026	-1.9499	4.0592	-0.1492	0.617	-0.1491	-0.5539	0.0792	-0.1636	0.0936	0.1978	0.0372	0.2048	-0.0467	0.0615	0.3513	-0.0734	0.1861	114.8399	56.3893	-7.539
30	0.7623	-0.1034	-0.0044	1.0298	0.3195	1.0569	-0.0485	0.2244	0.1694	-0.0783	-0.0055	0.0355	-0.0741	0.1121	0.0483	0.1484	-0.0123	-0.0228	0.1742	0.0485	0.1558	100.8346	71.3185	9.5762
31	2.5148	0.7289	-0.386	1.195	0.4678	1.7034	-0.0662	0.3903	0.3762	-0.221	0.043	0.1411	-0.1435	-0.0632	0.0388	0.2569	0.0238	-0.1093	0.1799	0.0377	0.257	80.7822	76.2024	5.3012
32	1.9318	0.0549	0.9024	0.3106	0.4086	0.8528	-0.1654	0.468	0.0665	-0.0959	0.1013	0.0179	-0.103	0.2341	0.0618	0.2195	-0.0399	0.0084	0.3311	-0.0113	0.2017	113.6729	53.6387	-0.3725
33	3.2648	0.3185	-0.25	4.1612	-1.3421	6.0954	-0.0079	-0.0369	-0.3571	0.0935	-0.0161	-0.3313	0.2446	0.5059	0.0359	0.1118	0.0539	-0.0318	0.2015	-0.0429	0.2695	130.3848	48.6908	19.6213
34	2.3821	0.1967	0.1084	2.4586	-0.0272	5.943	-0.0093	0.0692	-0.0244	0.0969	-0.0582	0.1372	-0.1154	-0.2321	0.0144	0.2028	-0.0484	-0.0081	0.1699	-0.0068	-0.0129	76.3203	53.9681	14.0078
35	0.2164	0.3764	0.3249	0.7683	0.648	0.5453	-0.0303	0.1765	0.1064	0.107	0.4014	0.0857	-0.3201	0.0918	-0.2095	0.2881	-0.0196	-0.025	0.2413	0.0227	0.2349	60.6087	40.9014	3.6328
36	1.8301	-0.6869	-1.1459	2.8234	-0.6747	7.1819	-0.0012	-0.0983	0.0606	-0.181	-0.0349	0.0262	0.2827	0.2468	-0.1072	0.2102	-0.0017	-0.0282	0.2209	-0.1298	0.2531	71.9296	77.0152	37.5577
37	5.0649	0.4886	0.1147	5.322	-1.0569	5.7896	-0.1307	-0.1792	0.1357	-0.1125	-0.2144	0.133	-0.0259	-0.4073	0.1671	0.361	0.0796	-0.152	0.4848	-0.2614	0.8779	52.4666	87.0296	44.2237
38	0.8397	0.6838	0.2806	5.8413	3.5809	3.4514	0.054	-0.1766	0.1791	-0.0077	-0.1391	0.0336	-0.1341	-0.0485	0.0695	0.2019	0.0447	-0.0685	0.1818	-0.078	0.0281	101.3575	72.5609	44.6218
39	0.8971	0.6798	-1.4037	0.541	-1.0496	2.2574	-0.1991	0.0257	-0.3018	0.0348	0.0831	-0.0192	0.2775	-0.102	0.1242	0.3309	0.0067	-0.0276	0.2634	0.0057	0.3826	117.3844	75.8819	60.5094
40	0.2104	0.2083	0.1357	0.3236	0.1634	0.2343	0.0488	0.0034	-0.0026	-0.0263	0.0247	-0.0169	-0.1492	0.0545	0.1549	0.2161	-0.0356	-0.0412	0.2516	-0.1479	0.1617	105.4099	63.377	12.9911
41	1.2273	0.6023	1.4637	1.3877	0.1017	3.7713	-0.1209	0.3824	0.0847	-0.1528	0.1314	0.1623	-0.2529	-0.1235	-0.0547	0.2614	-0.0087	0.0495	0.4315	-0.039	0.2983	124.6256	63.1425	0.6734

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -3 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 103 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 237 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 238 through 301 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 302 through 407 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 408 through 453 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 454 through 502 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 103 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 104 through 202 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 203 through 275 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 276 through 301 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 302 through 367 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 368 through 407 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 408 through 453 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 454 through 502 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 3 through 43 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 44 through 103 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 104 through 219 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 220 through 301 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 302 through 367 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 368 through 407 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 408 through 453 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 454 through 502 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 2 through 43 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 44 through 127 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 128 through 191 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 192 through 237 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 238 through 275 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 276 through 301 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 302 through 367 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 368 through 407 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 408 through 455 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 456 through 503 )
34	X-RAY DIFFRACTION	34	chain 'A' and (resid 512)
35	X-RAY DIFFRACTION	35	chain 'A' and (resid 513)
36	X-RAY DIFFRACTION	36	chain 'B' and (resid 512)
37	X-RAY DIFFRACTION	37	chain 'B' and (resid 513)
38	X-RAY DIFFRACTION	38	chain 'C' and (resid 512)
39	X-RAY DIFFRACTION	39	chain 'C' and (resid 513)
40	X-RAY DIFFRACTION	40	chain 'D' and (resid 512)
41	X-RAY DIFFRACTION	41	chain 'D' and (resid 513)

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 1278 molecules

-
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

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 6 types, 1278 molecules

-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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 1278 molecules

-
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