PDB-9ev5: Corynebacterium glutamicum CS176 pyruvate:quinone oxidoreductase ...

ID or keywords:

Entry

Database: PDB / ID: 9ev5

Title

Corynebacterium glutamicum CS176 pyruvate:quinone oxidoreductase (PQO) in complex with FAD and thiamine diphosphate-magnesium ion

Components

Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

Keywords

OXIDOREDUCTASE / Pyruvate:quinone oxidoreductase / pyruvate / carbon metabolism

Function / homology

Function and homology information

thiamine pyrophosphate binding / catalytic activity / magnesium ion binding
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.863 Å

Authors

Da Silva Lameira, C. / Muenssinger, S. / Yang, L. / Eikmanns, B.J. / Bellinzoni, M.

Funding support

France, 1items

Citation

Journal: Febs J. / Year: 2024
Title: Corynebacterium glutamicum pyruvate:quinone oxidoreductase: an enigmatic metabolic enzyme with unusual structural features.
Authors: da Silva Lameira, C. / Munssinger, S. / Yang, L. / Eikmanns, B.J. / Bellinzoni, M.

History

Deposition	Mar 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ev5.cif.gz	878.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9ev5.ent.gz	731.1 KB	Display	PDB format
PDBx/mmJSON format	9ev5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9ev5_validation.pdf.gz	4.3 MB	Display	wwPDB validaton report
Full document	9ev5_full_validation.pdf.gz	4.3 MB	Display
Data in XML	9ev5_validation.xml.gz	89.7 KB	Display
Data in CIF	9ev5_validation.cif.gz	132 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ev/9ev5 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/9ev5	HTTPS FTP

-
Related structure data

Related structure data	9ev3SC 9ev4C 9ev6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (9) #213 - Sep 2017 Sirtuins similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

B: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

C: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

D: Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: native gel electrophoresis, Homotetrameric enzyme (Schreiner and Eikmanns, J. Bacteriol. 187: 862-871, 2005)

Unit cell

Length a, b, c (Å)	104.192, 77.935, 158.044
Angle α, β, γ (deg.)	90, 100.63, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (Cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] / pyruvate:quinone oxidoreductase Mass: 62118.246 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: CS176 / Gene: Cgl2610 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8NMG5, pyruvate dehydrogenase (quinone)
#2: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1425 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.69 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M tri-sodium citrate, pH 6.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 2 / Wavelength: 0.9763 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 3, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 1.863→155.33 Å / Num. obs: 134984 / % possible obs: 94.7 % / Redundancy: 7.04 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC_1/2: 0.99 / CC_1/2 anomalous: -0.494 / R_merge(I) obs: 0.2038 / R_pim(I) all: 0.0826 / R_rim(I) all: 0.2201 / AbsDiff over sigma anomalous: 0.652 / B_aniso tensor eigenvalue 1: 0 Å² / B_aniso tensor eigenvalue 2: 10.6944 Å² / B_aniso tensor eigenvalue 3: 25.976 Å² / B_aniso tensor eigenvector 1 ortho1: 0.7702 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: 0.6377 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: -0.6377 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso tensor eigenvector 3 ortho3: 0.7702 / Aniso diffraction limit 1: 1.849 Å / Aniso diffraction limit 2: 2.03 Å / Aniso diffraction limit 3: 2.539 Å / Aniso diffraction limit axis 1 ortho1: 0.75693 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.65353 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.65353 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.75693 / Net I/σ(I): 5.83 / Num. measured all: 950618 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.5 / % possible ellipsoidal: 94.7 / % possible ellipsoidal anomalous: 94.5 / % possible spherical: 64.9 / % possible spherical anomalous: 64.6 / Redundancy anomalous: 3.59 / Signal type: local

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
5.912-155.33	7.12	0.0836	12.75	48058	48058	6749	6749	0.993	-0.707	0.0338	0.0903	0.349	100	100	100	100	100	3.76	100
4.677-5.912	6.85	0.1045	11.77	46202	46202	6749	6749	0.991	-0.642	0.0425	0.1129	0.431	100	100	100	100	100	3.54	100
4.077-4.676	6.86	0.1109	11.71	46283	46283	6750	6750	0.989	-0.624	0.0457	0.1201	0.462	100	100	100	100	100	3.52	100
3.7-4.077	6.75	0.1298	10.65	45576	45576	6749	6749	0.982	-0.554	0.0537	0.1407	0.526	99.9	100	99.9	100	99.9	3.47	100
3.433-3.7	7.11	0.1484	9.81	47957	47957	6749	6749	0.983	-0.597	0.0598	0.1601	0.545	99.8	100	99.8	100	99.8	3.63	100
3.228-3.433	7.21	0.1742	8.68	48640	48640	6749	6749	0.975	-0.51	0.0699	0.1879	0.601	99.8	100	99.8	100	99.8	3.68	100
3.065-3.228	7.29	0.216	7.52	49210	49210	6749	6749	0.961	-0.497	0.0862	0.2328	0.645	99.8	100	99.8	100	99.8	3.72	100
2.93-3.065	7.34	0.2663	6.29	49578	49578	6750	6750	0.957	-0.379	0.1057	0.2868	0.666	100	100	100	100	100	3.74	100
2.816-2.93	7.33	0.3346	5.44	49490	49490	6749	6749	0.938	-0.222	0.1326	0.3602	0.69	99.7	100	99.7	100	99.7	3.74	100
2.718-2.816	6.6	0.4049	4.42	44510	44510	6749	6749	0.911	-0.158	0.1702	0.4398	0.715	99.8	100	99.8	100	99.8	3.36	100
2.632-2.718	6.87	0.4826	3.95	46353	46353	6749	6749	0.902	-0.138	0.1984	0.5224	0.718	99.4	99.5	99.4	99.5	99.4	3.49	99.5
2.554-2.632	7.11	0.5539	3.62	47954	47954	6749	6749	0.879	-0.111	0.2231	0.5977	0.723	98	97.8	98	97.8	98	3.61	97.8
2.482-2.554	7.15	0.6067	3.37	48244	48244	6750	6750	0.871	-0.144	0.2436	0.6546	0.73	94.6	94.7	94.6	92.4	92.6	3.63	94.7
2.41-2.482	7.16	0.6599	3.11	48329	48329	6749	6749	0.839	-0.123	0.2647	0.7118	0.735	92.3	92.5	92.3	84	84.3	3.64	92.5
2.341-2.41	6.71	0.7307	2.75	45297	45297	6749	6749	0.824	-0.081	0.3041	0.7926	0.745	92	92.3	92	76.8	77.1	3.4	92.3
2.274-2.341	6.74	0.7646	2.67	45486	45486	6749	6749	0.772	-0.102	0.3173	0.8289	0.723	94.2	94.3	94.2	71.5	71.9	3.41	94.3
2.21-2.274	6.94	0.8247	2.51	46822	46822	6749	6749	0.77	-0.095	0.3369	0.8923	0.749	95.5	95.8	95.5	65.4	65.6	3.52	95.8
2.142-2.209	7.09	0.9804	2.17	47834	47834	6750	6750	0.705	-0.077	0.3951	1.0582	0.748	90.5	90.8	90.5	55.6	55.7	3.59	90.8
2.064-2.142	7.27	1.1735	1.86	49067	49067	6749	6749	0.655	-0.041	0.4662	1.2638	0.749	83.7	84.1	83.7	42.3	42.3	3.69	84.1
1.863-2.064	7.37	1.3613	1.59	49728	49728	6749	6749	0.563	-0.046	0.5382	1.4647	0.752	66.6	66.4	66.6	12.3	12.2	3.74	66.4

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.4	refinement
autoPROC	1.0.5 20221121	data processing
Aimless	0.7.9	data scaling
autoPROC	2.3.90	data processing
autoPROC		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 9EV3

9ev3

Resolution: 1.863→155.33 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.893 / SU R Cruickshank DPI: 0.249 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.259 / SU R_free Blow DPI: 0.193 / SU R_free Cruickshank DPI: 0.192

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2395	6723	-	RANDOM
R_work	0.2068	-	-	-
obs	0.2085	134984	64.9 %	-

Displacement parameters

B_iso mean: 32.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.54 Å²	0 Å²	-4.2983 Å²
2-	-	-1.2832 Å²	0 Å²
3-	-	-	-6.2568 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: LAST / Resolution: 1.863→155.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17098	0	320	1425	18843

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	17766	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.95	24225	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		5952	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		3124	HARMONIC	5
X-RAY DIFFRACTION	t_it		17766	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		2396	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		16454	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	3.3
X-RAY DIFFRACTION	t_other_torsion	16.51

LS refinement shell

Resolution: 1.863→2 Å

	R_factor	Num. reflection	% reflection
R_free	0.2708	125	-
R_work	0.2573	-	-
obs	-	-	6.91 %

Refinement TLS params.

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	1.1141	-0.1641	0.1307	0.7383	-0.1627	0.7204	-0.0254	0.1139	-0.0644	0.1139	0.0078	-0.0371	-0.0644	-0.0371	0.0175	0.1522	0.0105	-0.0957	-0.0787	-0.0162	-0.0947	21.2785	20.0812	57.2174
2	3.0232	1.1422	-1.1454	3.9093	-2.2878	2.7238	0.0348	0.0223	-0.0767	0.0223	0.0052	-0.2127	-0.0767	-0.2127	-0.04	0.1029	0.0199	-0.0778	-0.0431	-0.016	-0.1496	10.9143	20.8644	55.3019
3	1.3384	-0.576	-0.0429	0.9179	-0.2696	0.6186	-0.1422	0.2263	0.1152	0.2263	0.1457	-0.2026	0.1152	-0.2026	-0.0035	0.0733	-0.0305	-0.0219	-0.0848	0.0324	-0.0203	8.9801	-9.1529	63.9645
4	2.857	-1.3141	0.4107	1.3014	-0.0093	0.9987	-0.06	0.0036	0.2294	0.0036	0.0452	-0.1556	0.2294	-0.1556	0.0147	0.1078	-0.07	-0.0421	-0.1489	0.0153	0.1176	11.6291	-17.4187	56.7367
5	1.2746	-1.3771	-0.0403	1.4501	-0.0256	-0.0287	-0.0497	0.2873	0.1285	0.2873	0.0604	0.1828	0.1285	0.1828	-0.0107	0.2209	0.0401	-0.1047	-0.1682	0.1088	-0.0545	34.707	-20.4403	68.69
6	0.406	-0.0451	0.2368	0.8087	-0.1801	0.6237	0.018	0.1736	0.0318	0.1736	-0.0244	0.0644	0.0318	0.0644	0.0064	0.1638	0.0002	-0.1256	-0.0813	0.0356	-0.0638	37.4716	0.4064	66.029
7	0.5723	-0.156	-0.2075	1.0366	-0.0042	1.1695	-0.0003	-0.0273	0.0943	-0.0273	0.0521	-0.0208	0.0943	-0.0208	-0.0518	0.1004	0.0153	-0.086	-0.1607	0.0706	-0.0383	34.0827	-14.5333	61.0634
8	1.7357	0.3127	0.1284	1.848	0.1814	1.9825	0.0336	-0.0735	0.1671	-0.0735	0.0014	0.1791	0.1671	0.1791	-0.035	0.1092	0.0282	-0.071	-0.0692	-0.0211	-0.0893	44.5381	3.854	38.2083
9	1.4319	0.6178	-0.0917	0.7457	0.0579	0.5436	-0.0364	-0.1146	0.0064	-0.1146	0.0197	-0.0423	0.0064	-0.0423	0.0167	0.1357	0.0023	-0.0761	-0.0463	-0.0235	-0.0999	31.8858	6.7048	36.2872
10	1.068	-0.0651	0.1127	5.1359	0.6271	1.509	0.0246	-0.3175	-0.0942	-0.3175	-0.0718	0.093	-0.0942	0.093	0.0472	-0.0063	-0.0291	0.0274	0.0509	0.0508	-0.2986	36.9536	24.0372	18.5128
11	1.8516	-0.008	0.4502	1.225	0.0074	2.2785	-0.0051	-0.2215	-0.3404	-0.2215	0.0076	0.0958	-0.3404	0.0958	-0.0025	0.17	-0.0073	-0.0188	-0.104	0.0857	-0.051	39.3724	42.8901	29.7156
12	0.626	0.635	-0.4434	0.3501	0.0943	2.1539	-0.0106	0.3111	-0.636	0.3111	0.0576	0.2206	-0.636	0.2206	-0.047	0.1497	-0.0894	-0.094	-0.1916	-0.0419	0.1029	50.2109	46.5409	50.4655
13	0.6325	-0.2367	-0.0675	0.7013	0.021	0.3497	0.0208	0.0696	-0.125	0.0696	-0.022	0.1498	-0.125	0.1498	0.0012	0.1339	-0.0338	-0.1171	-0.0823	-0.0001	-0.0245	46.708	25.1833	53.2639
14	0.9503	-0.3433	-0.1444	1.0717	-0.1016	0.8569	-0.0306	0.1279	-0.2735	0.1279	0.0339	0.1399	-0.2735	0.1399	-0.0033	0.1275	-0.0842	-0.1166	-0.1532	-0.0104	-0.0213	46.751	39.1848	51.9247
15	1.073	0.0873	-0.1321	0.7642	-0.1046	0.8171	-0.0186	-0.1819	0.0942	-0.1819	-0.011	-0.2585	0.0942	-0.2585	0.0296	0.068	-0.0376	-0.1284	0.1011	-0.1225	-0.1024	5.9394	-1.4979	28.7749
16	1.9118	0.2312	-0.8629	1.2166	-0.2929	3.2941	-0.0845	-0.021	0.2826	-0.021	0.0284	-0.2784	0.2826	-0.2784	0.0561	0.0827	-0.0417	-0.1047	-0.0252	-0.0736	-0.0847	11.1387	-6.2059	36.5938
17	1.892	-0.8043	-0.9339	0.9999	0.6463	1.716	-0.0073	-0.0338	-0.0391	-0.0338	-0.0606	-0.3142	-0.0391	-0.3142	0.0679	0.0201	-0.0484	-0.0904	-0.0786	0.0339	-0.0524	0.5514	-3.3305	55.6721
18	2.2551	-0.6515	0.3662	1.7031	-0.4386	1.9209	0.0113	0.1216	-0.0839	0.1216	0.0189	-0.3435	-0.0839	-0.3435	-0.0302	-0.002	0.0262	-0.0426	0.0376	-0.0147	-0.1053	-14.2321	12.7723	58.2239
19	1.703	-0.0255	-0.9903	0.8055	0.3292	1.8314	-0.0099	-0.0829	-0.1898	-0.0829	0.0278	-0.4901	-0.1898	-0.4901	-0.0179	-0.0982	0.0748	-0.1395	0.1777	-0.0196	-0.1001	-25.9153	17.2869	40.1494
20	1.3344	0.0219	0.0299	0.9211	-0.1402	0.7998	0.0403	-0.143	-0.0368	-0.143	-0.0337	-0.5299	-0.0368	-0.5299	-0.0066	-0.0399	0.0183	-0.1927	0.3248	-0.0607	-0.1812	-15.8985	13.5422	25.0578
21	1.5727	-0.0928	-0.3544	0	-0.1408	0.6901	0.0999	0.0229	-0.0346	0.0229	-0.012	-0.2883	-0.0346	-0.2883	-0.0879	-0.0019	0.1084	-0.1482	0.0336	0.0166	-0.1278	-20.8871	21.9865	40.4267
22	2.3961	0.579	-0.2044	1.7208	0.7501	1.6048	-0.0157	-0.1591	-0.2398	-0.1591	0.0302	-0.305	-0.2398	-0.305	-0.0145	0.0785	0.1054	-0.1433	0.11	0.1084	-0.243	4.19	32.2408	23.092
23	0.6547	-0.0444	0.0288	0.3378	0.452	0.7518	0.0418	-0.0943	-0.0006	-0.0943	0.0251	-0.1998	-0.0006	-0.1998	-0.0669	0.0988	0.0249	-0.1014	0.0902	0.0196	-0.1871	9.6003	21.952	31.2181
24	3.6808	2.5142	-0.7412	0.7264	-2.4046	1.8587	-0.024	-0.0024	-0.1257	-0.0024	0.0305	-0.1614	-0.1257	-0.1614	-0.0065	0.1208	0.0439	-0.1177	-0.0045	0.0589	-0.1487	15.3581	31.7694	31.4111
25	2.291	-1.684	-1.6333	2.102	1.5067	2.1851	0.1842	-0.2327	-0.2559	-0.2327	-0.0932	-0.1069	-0.2559	-0.1069	-0.091	0.0957	-0.0082	-0.0649	0.0179	0.0792	-0.2086	32.9654	28.8741	18.4301
26	2.6935	0.4231	-0.1471	1.6193	0.2196	1.9784	-0.0319	-0.391	0.0701	-0.391	-0.0295	-0.0148	0.0701	-0.0148	0.0614	0.1232	-0.0026	-0.0137	0.2655	-0.0477	-0.3188	33.6215	12.4762	3.6883
27	3.3275	1.047	1.2755	0.9971	-0.6214	0.3616	0.0028	-0.4757	-0.0613	-0.4757	0.0236	-0.0424	-0.0613	-0.0424	-0.0264	0.0894	-0.0312	-0.131	0.5343	-0.3142	-0.4606	15.7749	3.2949	-8.8908
28	1.1599	-0.4056	0.8854	1.7271	0.5116	1.4892	0.0554	-0.2795	0.0572	-0.2795	-0.0596	-0.1007	0.0572	-0.1007	0.0041	0.0501	0.0452	-0.1446	0.3977	-0.0076	-0.3469	10.1337	17.0577	4.6238
29	0.0228	1.399	-0.1744	0.3679	-0.178	1.2124	0.1596	-0.2137	0.1305	-0.2137	-0.0857	-0.3475	0.1305	-0.3475	-0.0739	0.0192	0.0279	-0.233	0.3726	-0.1158	-0.3505	1.0512	10.32	8.8837
30	2.3758	-0.0536	0.7225	1.5024	-0.0841	3.4356	0.0923	-0.2403	0.1129	-0.2403	0.0282	-0.0428	0.1129	-0.0428	-0.1206	-0.1048	-0.009	-0.1956	0.4668	-0.2688	-0.4456	-2.0007	6.12	1.4325
31	3.7539	0.6454	-1.3634	1.6623	-0.9365	4.3205	0.0688	-0.3731	0.397	-0.3731	0.0301	0.1418	0.397	0.1418	-0.0989	-0.0557	0.0188	-0.0952	0.3198	-0.3388	-0.5315	23.2426	2.4255	-2.1607

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|2 - 132 }	A	2 - 132
2	X-RAY DIFFRACTION	2	{ A\|133 - 164 }	A	133 - 164
3	X-RAY DIFFRACTION	3	{ A\|165 - 250 }	A	165 - 250
4	X-RAY DIFFRACTION	4	{ A\|251 - 328 }	A	251 - 328
5	X-RAY DIFFRACTION	5	{ A\|329 - 371 }	A	329 - 371
6	X-RAY DIFFRACTION	6	{ A\|372 - 519 }	A	372 - 519
7	X-RAY DIFFRACTION	7	{ A\|520 - 576 }	A	520 - 576
8	X-RAY DIFFRACTION	8	{ B\|2 - 63 }	B	2 - 63
9	X-RAY DIFFRACTION	9	{ B\|64 - 164 }	B	64 - 164
10	X-RAY DIFFRACTION	10	{ B\|165 - 200 }	B	165 - 200
11	X-RAY DIFFRACTION	11	{ B\|201 - 328 }	B	201 - 328
12	X-RAY DIFFRACTION	12	{ B\|329 - 371 }	B	329 - 371
13	X-RAY DIFFRACTION	13	{ B\|372 - 506 }	B	372 - 506
14	X-RAY DIFFRACTION	14	{ B\|507 - 577 }	B	507 - 577
15	X-RAY DIFFRACTION	15	{ C\|2 - 132 }	C	2 - 132
16	X-RAY DIFFRACTION	16	{ C\|133 - 164 }	C	133 - 164
17	X-RAY DIFFRACTION	17	{ C\|165 - 200 }	C	165 - 200
18	X-RAY DIFFRACTION	18	{ C\|201 - 328 }	C	201 - 328
19	X-RAY DIFFRACTION	19	{ C\|329 - 400 }	C	329 - 400
20	X-RAY DIFFRACTION	20	{ C\|401 - 519 }	C	401 - 519
21	X-RAY DIFFRACTION	21	{ C\|520 - 577 }	C	520 - 577
22	X-RAY DIFFRACTION	22	{ D\|2 - 63 }	D	2 - 63
23	X-RAY DIFFRACTION	23	{ D\|64 - 132 }	D	64 - 132
24	X-RAY DIFFRACTION	24	{ D\|133 - 164 }	D	133 - 164
25	X-RAY DIFFRACTION	25	{ D\|165 - 200 }	D	165 - 200
26	X-RAY DIFFRACTION	26	{ D\|201 - 328 }	D	201 - 328
27	X-RAY DIFFRACTION	27	{ D\|329 - 371 }	D	329 - 371
28	X-RAY DIFFRACTION	28	{ D\|372 - 429 }	D	372 - 429
29	X-RAY DIFFRACTION	29	{ D\|430 - 476 }	D	430 - 476
30	X-RAY DIFFRACTION	30	{ D\|477 - 542 }	D	477 - 542
31	X-RAY DIFFRACTION	31	{ D\|543 - 577 }	D	543 - 577

-
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://pdbjlvh1.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

-
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

-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

-
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