PDB-8oz8: Crystal Structure of an Hydroxynitrile lyase variant (H96A) from ...

ID or keywords:

Entry

Database: PDB / ID: 8oz8

Title

Crystal Structure of an Hydroxynitrile lyase variant (H96A) from Granulicella tundricola

Components

Cupin 2 conserved barrel domain protein

Keywords

LYASE / Hydroxynitrile lyase / cupin / beta-barrel / ozonolysis / peroxidase

Function / homology

Function and homology information

(R)-mandelonitrile lyase / lyase activity / metal ion binding
Similarity search - Function

Biological species

Granulicella tundricola (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Bento, I. / Coloma, J. / Hagedoorn, P.-L. / Hanefeld, U.

Funding support

1items

Citation

Journal: Acs Catalysis / Year: 2023
Title: Can a Hydroxynitrile Lyase Catalyze an Oxidative Cleavage?
Authors: Coloma, J. / Hagedoorn, P.L. / Bento, I. / Hanefeld, U.

History

Deposition	May 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8oz8.cif.gz	384.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8oz8.ent.gz	262 KB	Display	PDB format
PDBx/mmJSON format	8oz8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8oz8_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8oz8_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8oz8_validation.xml.gz	29.1 KB	Display
Data in CIF	8oz8_validation.cif.gz	42.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oz/8oz8 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/8oz8	HTTPS FTP

-
Related structure data

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	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Cupin 2 conserved barrel domain protein

B: Cupin 2 conserved barrel domain protein

C: Cupin 2 conserved barrel domain protein

D: Cupin 2 conserved barrel domain protein

hetero molecules

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

1

A: Cupin 2 conserved barrel domain protein

B: Cupin 2 conserved barrel domain protein

C: Cupin 2 conserved barrel domain protein

D: Cupin 2 conserved barrel domain protein

hetero molecules

A: Cupin 2 conserved barrel domain protein

B: Cupin 2 conserved barrel domain protein

C: Cupin 2 conserved barrel domain protein

D: Cupin 2 conserved barrel domain protein

hetero molecules

defined by author
Evidence: light scattering, SEC-MALS
117 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Cupin 2 conserved barrel domain protein

B: Cupin 2 conserved barrel domain protein

C: Cupin 2 conserved barrel domain protein

D: Cupin 2 conserved barrel domain protein

hetero molecules

A: Cupin 2 conserved barrel domain protein

B: Cupin 2 conserved barrel domain protein

C: Cupin 2 conserved barrel domain protein

D: Cupin 2 conserved barrel domain protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	152.049, 152.049, 109.920
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22
Space group name Hall	P6₅2(x,y,z+1/12)

Components on special symmetry positions

ID	Model	Components
1	1	A-433- HOH
2	1	A-444- HOH
3	1	B-471- HOH
4	1	C-438- HOH
5	1	C-452- HOH

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Cupin 2 conserved barrel domain protein Mass: 14200.868 Da / Num. of mol.: 4 / Mutation: H96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Granulicella tundricola (bacteria) / Gene: AciX9_0562 / Production host: Escherichia coli (E. coli) / References: UniProt: E8WYN5

-
Non-polymers , 7 types, 660 molecules

#2: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#3: Chemical	ChemComp-NM2 / 3-CARBOXY-N,N,N-TRIMETHYLPROPAN-1-AMINIUM Mass: 146.207 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₁₆NO₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₄
#6: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.23 Å³/Da / Density % sol: 61.9 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: KBr, PEG 2000 MME, natrium citrate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.9763 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 1.85→131.68 Å / Num. obs: 64090 / % possible obs: 100 % / Redundancy: 11.1 % / B_iso Wilson estimate: 25.22 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.246 / R_pim(I) all: 0.111 / R_rim(I) all: 0.27 / Net I/σ(I): 8.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
9.06-131.68	9.6	0.065	656	0.997	0.028	0.071	99.8
1.85-1.89	11.5	2.258	3897	0.563	1.001	2.472

-
Processing

Software

Name	Version	Classification
REFMAC	1.20.1_4487	refinement
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→65.84 Å / SU ML: 0.1963 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.6401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1951	3232	5.05 %
R_work	0.1638	60806	-
obs	0.1653	64038	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.78 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→65.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4008	0	72	646	4726

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0054	4225
X-RAY DIFFRACTION	f_angle_d	0.7548	5763
X-RAY DIFFRACTION	f_chiral_restr	0.0545	596
X-RAY DIFFRACTION	f_plane_restr	0.0075	757
X-RAY DIFFRACTION	f_dihedral_angle_d	10.4233	594

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 (%)
1.85-1.88	0.3371	137	0.2902	2624	X-RAY DIFFRACTION	99.96
1.88-1.91	0.3209	131	0.2701	2592	X-RAY DIFFRACTION	99.93
1.91-1.94	0.2669	124	0.2404	2616	X-RAY DIFFRACTION	100
1.94-1.97	0.2488	152	0.2288	2598	X-RAY DIFFRACTION	99.96
1.97-2.01	0.2657	165	0.2032	2569	X-RAY DIFFRACTION	99.96
2.01-2.05	0.2306	170	0.192	2568	X-RAY DIFFRACTION	99.96
2.05-2.09	0.1964	140	0.182	2614	X-RAY DIFFRACTION	100
2.09-2.13	0.2083	141	0.1739	2609	X-RAY DIFFRACTION	99.96
2.13-2.18	0.2094	147	0.1719	2609	X-RAY DIFFRACTION	99.96
2.18-2.24	0.2207	139	0.1701	2609	X-RAY DIFFRACTION	100
2.24-2.3	0.2111	126	0.161	2623	X-RAY DIFFRACTION	99.96
2.3-2.37	0.2382	149	0.1637	2617	X-RAY DIFFRACTION	100
2.37-2.44	0.2248	126	0.1581	2643	X-RAY DIFFRACTION	99.89
2.44-2.53	0.2056	141	0.1564	2622	X-RAY DIFFRACTION	100
2.53-2.63	0.2065	136	0.1608	2629	X-RAY DIFFRACTION	99.96
2.63-2.75	0.2029	121	0.1554	2665	X-RAY DIFFRACTION	100
2.75-2.9	0.1928	138	0.1561	2648	X-RAY DIFFRACTION	100
2.9-3.08	0.1905	132	0.1696	2674	X-RAY DIFFRACTION	100
3.08-3.31	0.194	134	0.1585	2660	X-RAY DIFFRACTION	99.96
3.31-3.65	0.1807	137	0.1539	2682	X-RAY DIFFRACTION	100
3.65-4.18	0.1657	166	0.14	2687	X-RAY DIFFRACTION	99.96
4.18-5.26	0.1306	140	0.1186	2740	X-RAY DIFFRACTION	100
5.26-65.84	0.1926	140	0.1843	2908	X-RAY DIFFRACTION	99.74

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	4.68564483102	5.02360876933	6.55633405762	6.07528821553	6.4114726515	9.76704031672	0.30349364338	0.181456737466	-0.321846700828	0.210984731877	0.20670598492	-0.19489135321	-0.070363611668	0.330950403317	-0.483646945	0.254365568268	0.00425058705841	-0.0442760565667	0.230800279692	0.0100423230977	0.334931175704	42.9747438312	5.58669452278	-3.74876829497
2	7.48602827064	-4.65472576003	-2.20451606674	3.41185538294	1.8860522833	1.18223582154	-0.290830749108	0.159871623637	-0.663076904779	0.332692558454	0.0029798966871	0.296518312453	0.415152313037	-0.254963124386	0.2690475502	0.259217256138	-0.0168250769533	0.027920847534	0.246727579654	0.0591148441757	0.423160335217	20.2423269628	9.75033919487	1.81403951491
3	4.94038576733	-1.61722045349	3.92960661842	0.983945325029	-0.753773300941	4.73323284841	0.137939036697	-0.135314540268	-0.395411307915	0.105173555465	0.0682760079568	0.0998881911175	0.158873184126	0.0779265428339	-0.237680743824	0.219685124714	-0.00273230782112	0.00229290047023	0.211900330259	0.0541241352859	0.277628862888	34.2864280447	10.9707024134	3.96120389309
4	2.10936064097	-0.849574695372	0.422485318855	0.875717253741	-0.00173273671544	1.08828202346	-0.0796239260882	-0.111913785837	-0.211370635083	0.122042966914	0.0918420579252	0.13805288932	0.0300277267336	-0.0396149722988	-0.0506984954817	0.219994563808	0.00784063154696	0.042581154077	0.209638904877	0.0442057404554	0.24917852719	24.7824174769	21.3076612341	5.10778805602
5	2.11075596266	0.309673430303	0.170726749476	0.992199922354	0.0110723243864	0.167065374041	-0.0337928505202	-0.176520904011	-0.0593642294725	0.172828989049	0.0895719473565	0.214515961412	-0.0420443218355	-0.0346998881485	-0.0455091231836	0.244041053955	0.0265268856785	0.0379249767793	0.209438513635	0.0361556317605	0.267590735521	26.5432338405	24.0950513283	5.06080045277
6	6.15486608505	-5.34810538886	4.6063546012	7.09518618917	-3.22669587223	5.20743518314	-0.0640143386825	-0.943117595414	-1.34614925425	0.190404709919	0.319296137802	-0.0923358275695	0.578153716191	0.142807135586	-0.133076888283	0.390966532763	0.065348202154	0.127194493018	0.352963423079	0.143600627287	0.597622220702	28.2316482144	11.267818929	15.3101893633
7	2.34530738706	3.01644195699	-4.37558118748	3.97442369006	-5.73948866632	8.28355769161	-0.0228933373791	0.209630111343	0.470558300179	0.175541002436	0.164839086599	0.894919591823	-0.243066550659	-0.74840318326	-0.411191930659	0.232359659277	0.0340091260603	0.0151566482228	0.31404269223	0.0473609935673	0.425788015598	12.6078585307	23.3013140297	5.26484871645
8	1.18087650227	1.66399004108	-1.1930225729	2.83889406504	-2.64946111962	3.09542238848	0.0898596079325	-0.107500848198	0.0268516253264	0.427331874759	0.0197429319363	0.406754033953	-0.314476043706	-0.0374178704824	-0.121434143193	0.325879267506	-0.0022537693485	-0.0186644453436	0.282398826133	-0.0230546320513	0.238437429223	41.320266295	66.4883679521	23.7671313158
9	2.8578534752	1.89668332766	2.69247299944	5.06140854631	4.34616930282	4.26784180779	0.110010919223	-0.357150880466	0.0461465880413	0.253114919997	-0.152883066573	0.084171326372	-0.0999708290581	-0.359691460639	0.0563753481849	0.281698173909	-0.0362361046279	0.025186991568	0.277153707372	0.0184253620451	0.171844069269	29.3179162877	47.8713611059	15.3270474925
10	1.08704752999	-2.09243647479	0.148480588243	8.4143132492	1.93837264886	1.40609365199	-0.0374549766126	-0.185260538436	0.0822098516445	0.45515911306	-0.00712453874454	0.217934668259	0.00624014310691	-0.125338052265	0.0216452437043	0.230744906245	-0.0260747223366	0.0465141480558	0.24124825356	-0.023305547345	0.219276212752	32.8683243234	61.7319958429	15.3731794752
11	2.50842551306	-0.131349078214	0.330367339113	1.74241254554	-0.00700860927551	1.00277700356	-0.0105090920624	0.099580328483	0.129251702145	-0.0518171476397	-0.0298374413245	0.0715277578919	-0.0344433013492	-0.0576896784981	0.0439710575756	0.204430195719	-0.00641381691891	0.00414334908683	0.202451064073	-0.0150202618632	0.167380397281	32.4509324061	54.5638140287	2.67008971677
12	1.52743936224	3.49508785984	2.07968447522	8.65446674803	4.43229746689	3.33358575208	0.124420555179	-0.392288406564	0.396956743534	0.414456564306	-0.530450188183	0.883315246275	-0.00403463697636	-0.456720537825	0.40296561715	0.259401903788	-0.0306492406941	0.0592218325163	0.318127046535	-0.0508876000344	0.292939207466	21.2632491696	56.0822862766	9.53157912748
13	3.08568939293	0.335247772338	2.75076317668	7.17067686763	3.04963536266	3.54660419793	0.12788885529	1.26770236296	-1.19794340268	-0.798211837947	0.198812174773	-0.221287994958	0.227958451624	0.336164984005	-0.291587559283	0.349593010381	-0.00510602874365	0.00608852920434	0.385305822272	-0.0390919103729	0.301697623441	28.9814108888	40.8440846608	-1.93858176513
14	5.32926496378	4.79667809427	-5.24975160159	4.77011289067	-4.41785526575	5.32018931395	0.0660567393201	-0.325166420337	-0.0502435513757	0.339767102392	-0.00712459818491	0.0333128145262	-0.0564777568449	0.13122079109	-0.0348933380312	0.254555914872	0.0153983829294	0.0157400390707	0.176730281942	-0.0116888387598	0.222387526957	34.78063575	32.5157341316	4.50176863178
15	5.69373624374	-4.63699793262	-1.59011825368	5.64412554964	1.84615403951	3.85515600847	-0.0308251533999	-0.19072483591	0.498882746414	0.313315592293	0.044081528774	-0.0689751698591	-0.141114175711	0.10874925713	-0.00358462509109	0.201122025848	-0.0318549747622	0.0141768928759	0.208506557451	-0.0255719526288	0.223020994715	57.6359363506	28.0251255765	0.776203842247
16	6.30466240825	0.696189205349	-5.94604446201	2.35630142861	-1.73260856841	6.06081486534	0.162095547416	-0.43199743799	0.140336133725	0.286844754654	-0.00476859894141	0.133975487797	-0.297884076982	0.374471801787	-0.22143992879	0.214621784831	0.00488678806949	-0.00460289173958	0.215840219368	-0.0340209385516	0.18150573121	44.7034065896	24.9082381718	6.14966980597
17	1.26749820251	0.30681660846	-0.108493689907	0.552032988789	-0.593298035062	2.00178448328	-0.0260621384712	-0.0442058864678	-0.0909619739627	0.0400638422504	0.0785497542389	-0.0228380291017	0.0927015751844	0.119231419478	-0.0502804149217	0.184760259661	0.0316467373915	-0.00222935551869	0.186852988429	-0.0208945031664	0.184240854596	53.3635360186	15.9043835758	-0.76644267006
18	0.819589096917	0.327089180744	-0.280893843611	1.35296749518	-0.364974500595	2.349668192	-0.00309405162179	-0.085003068652	-0.0912374507986	0.076949730451	0.0194354765897	-0.0610082713789	0.17474284703	0.133135934265	-0.0472946964451	0.164393041377	0.0193164343891	-0.00800553346695	0.168441108997	-0.0110170261995	0.160714922802	51.4926538189	13.3272582206	-1.80839311723
19	7.60056698553	-1.38686053236	-4.56667876909	0.935206175431	1.19460601515	2.9200756092	-0.169491548251	-1.18651492959	0.250518645416	0.600931143488	0.203467489534	0.0280553306968	-0.31856014148	0.463629668341	-0.0297630106254	0.370650250378	0.0481103901727	0.0319444723958	0.374735107384	-0.0606610322062	0.198219325644	52.9585375627	19.9032087408	13.731240165
20	7.2549252531	0.632654423071	0.779816617553	3.69248306349	0.619801398978	2.67006761713	0.0551244570144	0.316909709274	-0.122588865767	-0.25982209598	0.0103733993473	-0.286122496336	0.663154057638	0.309088171664	-0.155521666164	0.239798204093	0.0404913011886	0.00894613732266	0.239216354355	-0.0122209606426	0.180199987588	64.8773207289	14.3549123459	-4.89738044645
21	5.65152718204	7.23643688725	-7.2432044859	9.72517104354	-8.68657361425	2.03099137566	-0.179793493771	-0.382100768456	-0.491044987401	0.103357431797	-0.0686254869226	-0.373481908788	0.0519705047139	0.540907445191	0.197986185417	0.314207273076	-0.0284206807594	-0.00629115657231	0.30081547735	-0.0599912853161	0.272920526991	53.2329063532	47.5082278287	-3.05085505074
22	0.847778806044	0.505481489981	-1.40506383688	4.92985071128	-4.71456993513	6.86469288552	0.141488312387	-0.0560951958565	-0.511238574673	-0.142596148349	0.0646094521779	0.0115054839142	0.948039257092	-0.0969772774311	-0.250758264778	0.35270860915	0.0114274674414	-0.0401703980592	0.165605397833	-0.0208227780555	0.279816167605	48.8787228339	37.9560999072	18.0581855043
23	4.99214394937	2.50253177017	-1.65332531882	1.46586203341	-1.46733400318	4.97687992981	-0.168877604248	0.34837929362	-0.533255533592	-0.0678057869391	0.0564061482864	-0.362630748058	0.340532576558	0.244909869247	0.15323808666	0.237411399658	0.0411275840556	-0.00693507079279	0.1679520844	-0.034100374056	0.271977112245	57.2643258486	44.7275450309	8.83961001242
24	2.78205147869	0.237935641074	-0.0901818550309	2.05844454018	-0.17242945992	2.03778659815	0.0599584360546	-0.175765161823	-0.206174816334	0.265802684013	0.00527421441555	-0.283041707314	0.178467128718	0.160451398619	-0.0602402350496	0.266464583653	0.0145011572759	-0.0681849312879	0.19399227249	0.00879483287814	0.204308407214	56.4369786072	49.7387852623	22.6502431632
25	5.79864551199	5.32645388738	-3.60706375047	6.39936156651	-4.84492501134	3.8991957655	-0.589074374472	0.378984400526	-1.0352592134	-0.846928340576	0.255868296887	-1.11554725411	1.87964656042	0.865872689361	0.326686188612	0.672787748916	0.163406512472	-0.0566939885512	0.399970275522	-0.131951525816	0.552080103988	64.9732140317	37.8901699455	15.9513936787
26	7.23342099911	-2.56688614943	2.05337410084	8.44037444826	-3.12507710577	2.2679674261	-0.0319882802586	-1.11559521381	-0.503446253869	1.23940657894	0.417618369076	0.519134819552	0.164017848844	-0.473487437444	-0.402494399706	0.538566270933	0.00473543529551	-0.0767775102253	0.339033232471	0.098692428152	0.2116848659	50.9279528012	43.9134280162	33.0598762734

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 1 through 10 )	A	A	1 - 10	1 - 10
2	2	chain 'A' and (resid 11 through 22 )	A	A	11 - 22	11 - 22
3	3	chain 'A' and (resid 23 through 44 )	A	A	23 - 44	23 - 44
4	4	chain 'A' and (resid 45 through 72 )	A	A	45 - 72	45 - 72
5	5	chain 'A' and (resid 73 through 111 )	A	A	73 - 111	73 - 111
6	6	chain 'A' and (resid 112 through 121 )	A	A	112 - 121	112 - 121
7	7	chain 'A' and (resid 122 through 131 )	A	A	122 - 131	122 - 131
8	8	chain 'B' and (resid 1 through 10 )	B	D	1 - 10	1 - 10
9	9	chain 'B' and (resid 11 through 22 )	B	D	11 - 22	11 - 22
10	10	chain 'B' and (resid 23 through 44 )	B	D	23 - 44	23 - 44
11	11	chain 'B' and (resid 45 through 111 )	B	D	45 - 111	45 - 111
12	12	chain 'B' and (resid 112 through 125 )	B	D	112 - 125	112 - 125
13	13	chain 'B' and (resid 126 through 131 )	B	D	126 - 131	126 - 131
14	14	chain 'C' and (resid 1 through 10 )	C	G	1 - 10	1 - 10
15	15	chain 'C' and (resid 11 through 22 )	C	G	11 - 22	11 - 22
16	16	chain 'C' and (resid 23 through 44 )	C	G	23 - 44	23 - 44
17	17	chain 'C' and (resid 45 through 72 )	C	G	45 - 72	45 - 72
18	18	chain 'C' and (resid 73 through 111 )	C	G	73 - 111	73 - 111
19	19	chain 'C' and (resid 112 through 121 )	C	G	112 - 121	112 - 121
20	20	chain 'C' and (resid 122 through 131 )	C	G	122 - 131	122 - 131
21	21	chain 'D' and (resid 1 through 10 )	D	J	1 - 10	1 - 10
22	22	chain 'D' and (resid 11 through 22 )	D	J	11 - 22	11 - 22
23	23	chain 'D' and (resid 23 through 44 )	D	J	23 - 44	23 - 44
24	24	chain 'D' and (resid 45 through 111 )	D	J	45 - 111	45 - 111
25	25	chain 'D' and (resid 112 through 121 )	D	J	112 - 121	112 - 121
26	26	chain 'D' and (resid 122 through 131 )	D	J	122 - 131	122 - 131

-
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 , 7 types, 660 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 , 1 types, 4 molecules ABCD

-Non-polymers , 7 types, 660 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 , 1 types, 4 molecules ABCD

-
Non-polymers , 7 types, 660 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