[English] 日本語

Yorodumi

- PDB-7exz: DgpB-DgpC complex apo 2.5 angstrom -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 7exz

Title

DgpB-DgpC complex apo 2.5 angstrom

Components

AP_endonuc_2 domain-containing protein
DgpB

Keywords

LYASE / C-deglycosylation / sugar phosphate isomerase/epimerase

Function / homology

Domain of unknown function DUF6379 / Domain of unknown function (DUF6379) / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / metal ion binding / : / DUF6379 domain-containing protein / Xylose isomerase-like TIM barrel domain-containing protein

Function and homology information

Biological species

human intestinal bacterium PUE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Mori, T. / Senda, M. / Senda, T. / Abe, I.

Citation

Journal: Nat Commun / Year: 2021
Title: C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
Authors: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi ...
Abstract: C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and ...

History

Deposition	May 29, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 17, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	7exz.cif.gz	834.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7exz.ent.gz	615.4 KB	Display	PDB format
PDBx/mmJSON format	7exz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7exz_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	7exz_full_validation.pdf.gz	1.8 MB	Display
Data in XML	7exz_validation.xml.gz	69.4 KB	Display
Data in CIF	7exz_validation.cif.gz	96 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/7exz ftp://data.pdbj.org/pub/pdb/validation_reports/ex/7exz	HTTPS FTP

-
Related structure data

Related structure data	30808C 30809C 7bvrSC 7bvsC 7drdC 7dreC 7exbC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7bvr-d 2iub-1 6kd7-1 7exz-d 5m8s-d 7cnq-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#74 - Feb 2006 alpha-Amylase similarity (3)

-
Assembly

Deposited unit

A: AP_endonuc_2 domain-containing protein

B: DgpB

C: AP_endonuc_2 domain-containing protein

D: DgpB

E: AP_endonuc_2 domain-containing protein

F: DgpB

G: AP_endonuc_2 domain-containing protein

H: DgpB

hetero molecules

221 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: AP_endonuc_2 domain-containing protein

B: DgpB

C: AP_endonuc_2 domain-containing protein

E: AP_endonuc_2 domain-containing protein

F: DgpB

G: AP_endonuc_2 domain-containing protein

H: DgpB

hetero molecules

defined by author&software
Evidence: gel filtration
205 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: AP_endonuc_2 domain-containing protein

B: DgpB

D: DgpB

E: AP_endonuc_2 domain-containing protein

F: DgpB

G: AP_endonuc_2 domain-containing protein

hetero molecules

defined by author&software
166 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.516, 156.721, 158.931
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein	AP_endonuc_2 domain-containing protein Mass: 38457.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) human intestinal bacterium PUE (bacteria) Gene: dgpC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9WXL1
#2: Protein	DgpB Mass: 16062.067 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) human intestinal bacterium PUE (bacteria) Gene: dgpB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9WUX0

-
Non-polymers , 5 types, 504 molecules

#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: SO₄
#6: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris (pH 8.5), 24% PEG4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.5→46.89 Å / Num. obs: 75507 / % possible obs: 100 % / Redundancy: 6.9 % / B_iso Wilson estimate: 37.63 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.122 / Net I/σ(I): 12
Reflection shell	Resolution: 2.5→2.55 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.815 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4426 / CC_1/2: 0.664 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7BVR

7bvr

Resolution: 2.5→46.89 Å / SU ML: 0.2948 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2329	2007	2.66 %
R_work	0.1817	73407	-
obs	0.1831	75414	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 41.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→46.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14584	0	183	475	15242

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	15071
X-RAY DIFFRACTION	f_angle_d	0.9478	20391
X-RAY DIFFRACTION	f_chiral_restr	0.05	2172
X-RAY DIFFRACTION	f_plane_restr	0.0065	2615
X-RAY DIFFRACTION	f_dihedral_angle_d	16.0151	5524

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 (%)
2.5-2.56	0.3373	146	0.2591	5162	X-RAY DIFFRACTION	99.98
2.56-2.63	0.3498	138	0.2332	5209	X-RAY DIFFRACTION	99.98
2.63-2.71	0.2838	145	0.2187	5173	X-RAY DIFFRACTION	100
2.71-2.8	0.2681	138	0.2094	5202	X-RAY DIFFRACTION	100
2.8-2.9	0.2866	146	0.2091	5178	X-RAY DIFFRACTION	100
2.9-3.01	0.2439	143	0.1974	5186	X-RAY DIFFRACTION	100
3.01-3.15	0.2904	138	0.2013	5202	X-RAY DIFFRACTION	100
3.15-3.32	0.2249	141	0.1827	5233	X-RAY DIFFRACTION	99.96
3.32-3.52	0.2565	141	0.1846	5208	X-RAY DIFFRACTION	100
3.52-3.8	0.2478	144	0.1755	5249	X-RAY DIFFRACTION	100
3.8-4.18	0.1996	142	0.1567	5253	X-RAY DIFFRACTION	100
4.18-4.78	0.1786	145	0.1517	5295	X-RAY DIFFRACTION	100
4.78-6.02	0.2018	146	0.1708	5339	X-RAY DIFFRACTION	100
6.02-46.89	0.1951	154	0.1715	5518	X-RAY DIFFRACTION	99.53

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	1.11971823847	-0.402867750258	0.206392223867	1.39287812558	-0.039327243216	0.563561654467	-0.0471792809566	-0.148248569588	-0.357125297128	0.0462627630033	0.0285275703302	0.177651528809	0.281300749815	-0.0318808785391	0.0100438140339	0.370199610066	-0.00730312520209	0.0391710199151	0.221248593677	0.0627173033698	0.329967323057	9.61533045467	-21.0183507007	-51.6732136049
2	1.96146564749	-1.64261731337	-0.473380607577	1.75484418188	0.970495630144	1.51664310684	-0.0466507388874	-0.054840457561	0.123938916524	-0.170031439401	-0.0144638619502	0.1418640167	0.190646440442	0.0311432931889	0.0505477260119	0.494574535114	0.0347041675301	0.177454067146	0.527471309986	0.262118065022	0.667919269922	-4.59050478343	-26.483212998	-24.3299135718
3	2.53280400433	0.307073253188	0.650241012496	2.55249393553	0.16480038792	3.41958610779	-0.0854961592626	-0.429122872113	-0.640944255512	0.318734860821	0.0792890214326	0.0555074061206	0.6205737957	0.186345359131	-0.00609976161001	0.472326895678	0.117566549651	0.111952911501	0.341655518555	0.141672298522	0.453191520076	13.1154496209	-32.8811711475	-38.2986540803
4	8.80585387561	1.19374628979	6.14194303367	2.68889192339	1.04339802922	4.29756178381	0.287217877338	-1.29924780612	-0.544356595185	0.246779230903	-0.517767474208	-0.240453537863	0.70713229062	-0.219379926305	0.246017936454	0.505132245228	0.0492694835536	0.0819629895035	0.417023930379	0.104985995255	0.262199174651	3.07141672728	-7.73925294607	-33.0113380388
5	1.65195332295	0.556734772367	-0.337969111176	3.0095227905	-0.892329257897	3.34873349408	-0.0094982745414	-0.181861749051	-0.137839902899	0.297224661521	-0.0251741636733	-0.247608394579	0.0318311302642	0.178303222861	0.0405431570989	0.186626385325	0.0140769394444	0.0183576574282	0.218773265648	0.0045556837904	0.189889760289	7.09179493096	7.89943835068	-39.8547566758
6	2.84778498945	-1.39889492285	-0.603741417591	5.15246919446	5.69100094973	6.81444687169	0.0878064076325	-0.118482341226	0.0984089875107	0.208221635106	-0.238711604196	-0.0893432137578	0.0487530689836	-0.259023173957	0.0245480264308	0.31120702899	0.0207593158213	0.00298403720015	0.26245913302	0.076790308693	0.274894942073	-2.51775440916	6.97546368464	-41.3317907638
7	0.420421136894	-0.553313288311	0.357137816521	2.25104743964	0.896035515753	1.86413437892	-0.000635128441533	0.0184247771112	0.0337512495936	-0.273979069555	0.0683354883742	-0.168026316449	-0.23210038567	-0.0435644981385	-0.0762024473107	0.225085839268	-0.00639652087415	0.0312880095713	0.213985166268	0.0380700792171	0.233011300115	2.89489646558	3.22216539053	-48.1266600207
8	2.00736137514	-6.97945614716	7.27329453762	5.95715691116	-2.10556583847	2.01406549653	0.0643233758759	-0.130429583522	0.565506963704	0.0670194494043	-0.406702591422	-0.672287951545	-0.291859803989	0.00819183132106	0.324387340048	0.454897274866	-0.0121471635518	-0.00980198331433	0.333908901787	0.0124643023813	0.339340497519	3.82414723574	21.0724092156	-33.0814486347
9	1.7799251649	2.13108447937	-0.038726253536	7.07125901011	2.90011830438	1.7513047879	-0.00982030599791	-0.274721052258	0.0305728712473	0.472650396406	-0.0887859245376	0.329732002656	0.410743123847	0.0776846268103	0.0833311016456	0.358732844834	0.00564453154624	-0.00313863571862	0.379781813856	0.0732425272653	0.244827332227	-1.44269289071	-1.84892248174	-37.2095150654
10	3.60251232892	1.15327441246	-0.719530423317	5.3758475705	6.962888423	2.06711462678	0.43066070913	-0.502677985622	-0.460564711867	0.872635153783	-0.878759686393	0.510570611328	0.839211338664	-1.11864221238	0.466272388945	0.441918412834	-0.116921711193	-0.0123214731662	0.379638263087	0.0888980486299	0.369462535762	-7.7299718899	-11.9880608081	-41.3543466341
11	1.53552675621	-1.30374216066	2.6676578516	5.93129591503	2.88826488937	2.01073555723	0.2229985152	-0.276854743921	-0.120665235247	1.09386632877	0.152397178617	-0.761786870351	-0.0798612767706	0.30157397271	-0.480476683771	0.404190743897	-0.0559185819268	-0.0774849803841	0.381524234516	-0.0109069520236	0.233869059781	7.3396532701	10.3335220345	-28.4371515955
12	1.97090118128	-0.13751262682	-0.0473149309534	0.728924465777	0.272092337414	1.26925358634	0.0646442297089	-0.0105195825295	0.147251725295	0.0709996874912	-0.045742719446	-0.113354507863	-0.18032101452	0.0421525835449	-0.029051281496	0.301773985358	-0.0353809874016	0.00826763177231	0.220346044536	0.00270762984261	0.284949575425	29.7194594327	22.2475783505	-49.2308009268
13	2.92551249429	0.852555736128	0.141848403405	3.27089221031	2.14803526426	6.4588386786	0.172076933534	-0.0972369029252	0.141620157676	0.179514908355	-0.130999776562	-0.455298638528	-0.568958352898	0.309592527225	-0.032305224825	0.330933511742	-0.0777843742554	-0.037312682174	0.238598383687	0.0322445654077	0.31298295382	41.1294565312	35.4099026352	-53.6271886186
14	0.971342077853	-0.972281106342	-0.487845182804	4.83019802402	-0.920737118181	5.11360855671	-0.182566180584	-0.163624734182	0.0919583397458	0.786424393151	-0.273000384875	-0.859316383491	-0.437514911506	1.22858705886	0.447096050021	0.604124607431	-0.181482547972	-0.196401225283	0.61239110818	0.103098933573	0.563468887566	49.7192346829	32.9160171726	-23.3264738901
15	3.58755955999	0.708634312283	0.0348690004265	2.13705598052	0.229690259933	3.51996875884	0.0440486646856	-0.321898540883	0.505052745388	0.42884426479	-0.139862411705	0.00957322051883	-0.729495230421	0.0994512450468	0.0852688540907	0.479934513306	-0.0489921190829	-0.0342442027215	0.258634353309	-0.0597674148701	0.35439984752	31.2776924383	38.2025999766	-36.7526824133
16	0.151069210831	0.459638054989	0.283752913998	2.18069533318	1.95129419658	2.38562426815	-0.124976947775	-0.0193687411402	-0.0338942970844	-0.0965679876955	0.0555950790588	0.270946657716	-0.123624988336	0.229546434933	0.054036689293	0.388688422539	0.0716666418618	-0.0938118385628	0.370649984006	0.0598707488131	0.371566630191	37.2420889131	-0.651540770882	-37.016749085
17	0.66246100695	0.909032449678	-0.273857151644	3.4419866408	0.852232238052	1.54035330843	0.119434919217	-0.191479177255	-0.103860223518	0.518054166	-0.150154992884	-0.530658210962	0.208166013522	0.380531011545	0.0416624661378	0.279914917796	-0.00424241474731	-0.0925386040252	0.35014337187	0.0636649961049	0.300680862661	42.1779759573	2.89794468878	-42.1599108981
18	7.77596235802	-3.44464626036	0.82084390505	8.91630600409	-3.62221426569	7.75819156633	0.0132505097562	-0.0248191606185	0.417864008722	-0.216648158691	-0.276331894167	-0.796647289638	0.74537362181	0.235861828841	0.283655057851	0.324568671246	0.0523705270912	-0.0297058480686	0.324671133025	0.0795681339021	0.32430638303	45.6509671373	-4.84566279865	-43.2862115757
19	0.667488614462	1.06110362528	-0.799424721878	2.75689408969	-0.280718848653	2.45048456267	0.0177676368004	-0.00438489212992	0.00462934126808	-0.064600828681	-0.203464986941	-0.0419412195215	0.190298830168	0.518779744663	0.191658273009	0.236776496192	0.0308622810451	-0.0585013115521	0.332339614344	0.0464333563612	0.230618561464	41.0902819478	2.73636469976	-49.0322623548
20	0.90026049115	0.264384443119	0.100905191462	4.44811336663	-3.64042083286	4.40488497406	0.239320897763	-0.399567888518	-0.212175503129	0.763617094353	-0.193810924919	-0.0838265352026	-0.00800063853805	0.235828382647	-0.0288603027033	0.32157803639	0.0670731696106	-0.0424017099643	0.42414190811	0.0536740040739	0.297705547766	43.9384821344	-4.54702053225	-35.5805503818
21	9.24563665497	1.2177362361	1.52090295761	5.47691812134	3.63608611977	2.46837437517	0.229647805692	-0.475307519434	0.204075136378	0.549456750865	-0.0688257162409	-0.489952137209	-0.0583746841559	0.536404521303	-0.195428189517	0.431797247911	-0.0859825537545	-0.114539343667	0.404260005791	0.00926076999357	0.369830665669	51.532742008	21.4733151055	-45.256570661
22	6.2646964803	4.7288250989	0.596165661218	9.61971490486	-2.0804018251	3.21118003301	0.471179736755	-1.03071526932	-0.472166063373	1.20482999301	-0.676656418189	-0.525305471841	-0.105876894683	0.281791371094	0.199138641773	0.34014948575	0.0177761907029	-0.0596245306079	0.464147289862	0.0129492867929	0.281130413374	41.1624332818	0.526824636967	-32.4029524627
23	1.81623904106	1.20229053903	-0.554574023144	0.861157904111	-0.339555252656	0.903402670265	0.0906730140392	-0.0352019713132	0.0694471017007	0.0661356612135	-0.0904272832705	0.0131478409007	-0.114342597839	0.0459883138528	-0.000908906687518	0.239026580044	0.028243312176	-0.011298846112	0.162209566573	0.0244686910261	0.237349206143	8.28334384789	18.8161071809	-68.522657773
24	2.14279664375	-0.879175083812	0.778799247921	2.17698672012	-2.27994098913	3.36031466848	0.0256706096253	0.0414079822441	-0.0799462307901	-0.0315940690939	0.03971378073	0.333466452891	0.00425770990527	-0.181727598802	-0.0658676818853	0.215016750167	0.0128996185233	-0.00610351864453	0.179822813697	-0.0368660105751	0.279251111721	-6.91875765734	23.2401962668	-60.1376994231
25	2.33085609221	1.13068967137	0.231029074543	2.72503432723	1.67568391489	1.44083407732	0.23112247283	0.0850007178392	-0.443439861878	-0.0972667485645	-0.196101476974	0.112530695499	0.0872455901831	-0.329313314506	-0.0409294959247	0.473134921894	0.0515896670563	-0.157942188057	0.444117106071	0.00493588582709	0.39670666696	-15.9132404556	21.2984798169	-91.2264223494
26	2.32866092324	-0.949389696216	-1.18716169641	0.961763794414	1.28804944154	5.32280664236	0.0918991018553	0.329083299781	0.416647172834	-0.0810912740139	-0.161039941751	0.0206693677394	-0.71771751933	-0.296032278583	0.0520352058883	0.34116669204	0.0300411732964	-0.0319081063524	0.213598556948	0.0526477871661	0.341975814958	-5.1719352081	35.1869974003	-76.6444122917
27	3.1669326691	-1.01940646594	-0.747902463085	4.3192357145	5.90924434537	8.28091639245	0.392127979973	0.267713138072	-0.113954831604	-0.479189174552	-0.177645948802	0.0861036434564	-0.371629119691	-0.492632859809	-0.215804796972	0.405737156315	0.0283109516313	-0.0640059037763	0.193976936623	0.0674707577271	0.286440076382	1.84362226181	27.6126332111	-76.3111855273
28	3.77576764414	-3.65124690148	-3.23116509134	9.61711648805	9.70254193001	9.95974171526	0.100025172873	-0.185903141617	0.100725274399	-0.783621709866	0.25100499615	-0.105311204521	-0.758274745348	0.486592496415	-0.335651768285	0.330462881326	0.00283556537831	0.0240419357369	0.293130657148	0.11237246341	0.36140249218	7.02005715613	34.1763705245	-81.6278094923
29	7.24652002352	1.06494738808	-4.44974322396	3.49775621992	-1.20274922049	2.81499683286	-0.24806158637	1.22173141845	0.330290906978	0.13789313562	0.395965787784	-0.0200903490341	-0.143993663705	-0.697248735782	-0.143942942959	0.434217708774	0.0381587519157	-0.192435603599	0.386622846323	0.0646445504017	0.331246524872	-0.772303380676	6.02048648701	-83.0526341433
30	4.6648189952	-2.79503825408	4.29382642212	2.87320054167	-4.575811837	7.49698329445	0.0835660829782	0.0792196058891	-0.0845571211268	0.406179516336	-0.253861726348	-0.28151339237	0.0726966472358	0.152669015322	0.155101918789	0.381873665134	-0.0164204869498	-0.00579890067671	0.19736137332	-0.0389032520722	0.289307858646	12.9791250549	-13.274685523	-77.8461362018
31	3.11611080916	-1.34988253442	-2.60950922765	9.88717269589	2.77604942004	2.63457432163	-0.179186476789	0.131551055406	-0.394619953814	-0.533691168392	0.0819611627463	0.561525431001	0.270206706501	-0.144008221026	0.0977629574683	0.317916094501	-0.0406878632637	-0.10347534387	0.247868676888	0.0154051565284	0.242506665457	0.473219199001	-4.53994319419	-74.2783187775
32	1.30656400801	-1.0964929984	-0.303461134299	3.99850399633	-0.266677119473	2.27621907964	-0.0188606364033	-0.116975406026	-0.175998411861	0.315951720553	-0.0181903428925	-0.109402384133	0.376956432733	-0.0477137230996	0.0362670969913	0.260204162941	-0.0342846663187	-0.0585502317726	0.178769762463	0.0201003928713	0.234467068128	3.93877280908	-3.9387789402	-68.0073179978
33	4.16806403698	2.05197468775	-3.72210806157	2.00322300835	1.9979139673	2.0127284525	-0.409968377833	0.447360768774	-0.484879359668	-0.643208388216	-0.80090604763	-1.00437219413	0.93775718556	0.359504978272	1.01998810691	0.674727032766	0.0136869260383	0.01978593022	0.226939341773	-0.0497065410657	0.649807938807	11.1404819933	-20.2754932552	-83.1407139365
34	2.567905252	-2.19863154693	-1.35841367631	4.1516179806	1.12912178695	2.61376615056	0.0588004055353	0.305442617568	-0.246528222295	-0.501856008389	-0.120668647723	0.553274097983	-0.0857923060507	-0.417394816612	0.0700632792676	0.285957826135	-0.0295292667305	-0.112875380614	0.257152712661	-0.000141849011619	0.332806973349	-5.86254963778	1.51237419945	-77.1654960713
35	8.62321872088	-5.33642858082	-4.61811323618	6.24037438823	2.44756066815	9.43833669833	0.420228525027	0.504364081683	-0.362171429159	-0.773065782721	-0.676454679015	-0.308278506136	0.302423010367	-0.0180872009855	0.233272814737	0.585362681321	0.00836025289804	0.0823564145154	0.308035711747	0.0433233840768	0.302996574315	11.0552599671	-9.68454737219	-87.1136992201
36	0.929668556308	0.418014682523	0.0433918020791	0.912132822377	-0.222955476822	1.14814144182	0.0515501685818	-0.0545210196745	-0.247643781897	-0.0179911575544	-0.0659834488447	-0.163793704616	0.239477910453	0.124647183184	0.0103847139434	0.323506760325	0.0589973814701	-0.00542274361931	0.247556259741	0.0258688236458	0.291276504542	36.0680304361	-11.1383409447	-68.1987242888
37	1.02323624846	-0.287276542422	-0.284002666351	1.44406167403	1.43748445253	1.46468145743	0.0884398055326	0.0133141821586	-0.0711662862004	0.00486228692507	0.0802099878151	-0.301640235337	0.1382152169	0.401550174689	-0.159980352325	0.427350844172	0.153543390303	0.0151846162515	0.505732004424	0.0896289966133	0.437986183412	51.5532720169	-18.5866125546	-64.432510273
38	5.60627825488	-0.604517469774	2.78628092327	4.81422746746	-4.45462065387	6.54288209409	-0.227627350302	-0.385431752784	0.450525567422	0.230359285318	-0.261851522971	-0.558907605531	-0.243458643738	1.46747479708	0.49296178841	0.501281322	0.0272631311092	0.0107893121153	0.740934614095	-0.0587176789952	0.345350534795	56.7485081378	-13.1976902693	-95.3222532258
39	1.91341666374	-1.67703038104	-1.1241158769	3.18769716598	-0.50757698985	2.19139277231	0.235329939895	0.255137044122	-0.367296715875	-0.452703689178	-0.277678371113	-0.138537357476	1.0847521685	0.785235546946	0.0389112483395	0.625059448565	0.213741460064	0.0243061973385	0.410328813136	-0.00184828176913	0.411351591005	47.2752940631	-27.3676956911	-80.2666961687
40	3.10187750265	-0.240505406477	-0.328397407318	9.02163082358	-6.01086514751	4.10216789823	-0.021661503658	0.175284210125	-0.283600792302	-0.390133262326	0.415959254674	0.689301050198	0.973383549757	0.195759518589	-0.416155715554	0.673747531777	0.0785500048255	0.0385772318178	0.264298939819	-0.0180720725197	0.365523094748	40.4991536844	-20.0008684365	-78.8632130745
41	9.92991932843	-2.60207671214	-1.81501016822	6.26780499922	4.91768812083	7.92842579456	-0.00502238192376	0.194543113557	-0.861256385567	-0.477631448805	0.0953917396052	0.221104791913	1.05813796844	-0.0816242664822	-0.0671294808646	0.520812536638	0.0272790293605	-0.0275275169948	0.299640341909	-0.0333425978318	0.306697356691	34.8922192549	-26.6054148677	-84.1916467356
42	1.11846271246	-1.86628445711	-1.25537644579	5.40459570138	2.59734178838	2.57186097135	-0.104124848846	0.112836811626	-0.0806757474665	0.0416893405755	-0.0235175401659	0.239614844046	0.202550795133	0.0519360807671	0.103523040837	0.268305243231	-0.00306042473055	0.0126705896552	0.302939673736	0.0600405180194	0.260312275485	33.5585773927	14.7955472248	-79.5164835757
43	2.75128382783	-1.26574034546	1.82512685784	2.16782123049	0.945404522096	4.37370951116	0.0466186748624	0.0655579611096	0.0492466323826	-0.0157593334988	-0.0654220342269	-0.0727191578661	-0.0451547517268	0.303433360488	0.0212482606343	0.204938020017	-0.0177530301313	0.0476515939877	0.206731516778	0.0431532894056	0.220246207832	40.5939664246	11.6776747949	-72.0705688414
44	7.29066865498	0.152841125688	3.91907792651	7.27608739132	6.90570375407	2.01447324227	0.780393678417	0.226201835752	-0.367188672289	-0.629514625133	-0.318422944219	0.430593464674	0.143491280295	-0.241312570045	-0.426640850362	0.502682609375	0.0771557986046	0.0431708491601	0.27460832386	0.127737646805	0.607544529344	30.5413969846	28.1407568244	-82.1808758932
45	2.1466898409	-7.16540811933	4.97699641828	2.15936647223	-8.02281656059	9.22779758598	0.239785063684	1.25314395127	0.29431968275	-0.693384023737	-0.878280142037	0.0823780488261	0.0744323143991	1.28240988621	0.644157652086	0.464464397276	-0.0854383582669	-0.0447682580678	0.4230855423	0.161852208493	0.480551553713	42.06350514	13.7720710371	-82.1462638646
46	4.34683418283	-2.91636173269	-4.94770766227	4.61552659154	0.822041451678	7.96523931481	0.131896183663	-0.204815756139	0.38759235714	-0.392873206487	0.225099176595	-1.11604259178	0.195763258101	1.15284566155	-0.437796415957	0.340847677314	0.0546859622154	0.0719226674513	0.437809150697	-0.0555649853904	0.429208919947	55.8759352834	-1.81047182708	-73.4012676646
47	8.93461154721	-7.61915420492	8.67012198977	8.41405417092	-6.32375287142	8.88213908224	0.230711167642	0.929070682187	0.422609432138	-0.587007397372	-0.516729329904	-0.317342427376	-0.0834896894228	0.326811867903	0.265264576897	0.36692330338	-0.0331772849994	0.0537240920302	0.272075261021	0.00765378543486	0.248885441471	37.2155003625	13.1119059129	-85.3082497026

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 177 )	A	A	2 - 177	1 - 176
2	2	chain 'A' and (resid 178 through 245 )	A	A	178 - 245	177 - 244
3	3	chain 'A' and (resid 246 through 325 )	A	A	246 - 325	245 - 324
4	4	chain 'B' and (resid 3 through 12 )	B	E	3 - 12	1 - 10
5	5	chain 'B' and (resid 13 through 43 )	B	E	13 - 43	11 - 41
6	6	chain 'B' and (resid 44 through 70 )	B	E	44 - 70	42 - 68
7	7	chain 'B' and (resid 71 through 97 )	B	E	71 - 97	69 - 95
8	8	chain 'B' and (resid 98 through 105 )	B	E	98 - 105	96 - 103
9	9	chain 'B' and (resid 106 through 121 )	B	E	106 - 121	104 - 119
10	10	chain 'B' and (resid 122 through 133 )	B	E	122 - 133	120 - 131
11	11	chain 'B' and (resid 134 through 141 )	B	E	134 - 141	132 - 139
12	12	chain 'C' and (resid 2 through 108 )	C	I	2 - 108	1 - 107
13	13	chain 'C' and (resid 109 through 177 )	C	I	109 - 177	108 - 176
14	14	chain 'C' and (resid 178 through 245 )	C	I	178 - 245	177 - 244
15	15	chain 'C' and (resid 246 through 324 )	C	I	246 - 324	245 - 323
16	16	chain 'D' and (resid 4 through 25 )	D	M	4 - 25	1 - 22
17	17	chain 'D' and (resid 26 through 54 )	D	M	26 - 54	23 - 51
18	18	chain 'D' and (resid 55 through 70 )	D	M	55 - 70	52 - 67
19	19	chain 'D' and (resid 71 through 97 )	D	M	71 - 97	68 - 94
20	20	chain 'D' and (resid 98 through 116 )	D	M	98 - 116	95 - 113
21	21	chain 'D' and (resid 117 through 128 )	D	M	117 - 128	114 - 125
22	22	chain 'D' and (resid 129 through 141 )	D	M	129 - 141	126 - 138
23	23	chain 'E' and (resid 2 through 90 )	E	P	2 - 90	1 - 89
24	24	chain 'E' and (resid 91 through 177 )	E	P	91 - 177	90 - 176
25	25	chain 'E' and (resid 178 through 245 )	E	P	178 - 245	177 - 244
26	26	chain 'E' and (resid 246 through 289 )	E	P	246 - 289	245 - 288
27	27	chain 'E' and (resid 290 through 307 )	E	P	290 - 307	289 - 306
28	28	chain 'E' and (resid 308 through 324 )	E	P	308 - 324	307 - 323
29	29	chain 'F' and (resid 3 through 12 )	F	T	3 - 12	1 - 10
30	30	chain 'F' and (resid 13 through 34 )	F	T	13 - 34	11 - 32
31	31	chain 'F' and (resid 35 through 70 )	F	T	35 - 70	33 - 68
32	32	chain 'F' and (resid 71 through 97 )	F	T	71 - 97	69 - 95
33	33	chain 'F' and (resid 98 through 105 )	F	T	98 - 105	96 - 103
34	34	chain 'F' and (resid 106 through 133 )	F	T	106 - 133	104 - 131
35	35	chain 'F' and (resid 134 through 142 )	F	T	134 - 142	132 - 140
36	36	chain 'G' and (resid 2 through 107 )	G	W	2 - 107	1 - 106
37	37	chain 'G' and (resid 108 through 177 )	G	W	108 - 177	107 - 176
38	38	chain 'G' and (resid 178 through 245 )	G	W	178 - 245	177 - 244
39	39	chain 'G' and (resid 246 through 289 )	G	W	246 - 289	245 - 288
40	40	chain 'G' and (resid 290 through 307 )	G	W	290 - 307	289 - 306
41	41	chain 'G' and (resid 308 through 325 )	G	W	308 - 325	307 - 324
42	42	chain 'H' and (resid 3 through 34 )	H	AA	3 - 34	1 - 32
43	43	chain 'H' and (resid 35 through 97 )	H	AA	35 - 97	33 - 95
44	44	chain 'H' and (resid 98 through 105 )	H	AA	98 - 105	96 - 103
45	45	chain 'H' and (resid 106 through 116 )	H	AA	106 - 116	104 - 114
46	46	chain 'H' and (resid 117 through 128 )	H	AA	117 - 128	115 - 126
47	47	chain 'H' and (resid 129 through 141 )	H	AA	129 - 141	127 - 139

+
About Yorodumi

-
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

-
Protein , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 5 types, 504 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

-Protein , 2 types, 8 molecules ACEGBDFH

-Non-polymers , 5 types, 504 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

-
Protein , 2 types, 8 molecules ACEGBDFH

-
Non-polymers , 5 types, 504 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