[English] 日本語

Yorodumi

- PDB-6tv0: Serratia spp. cyanase hydratase -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 6tv0

Title

Serratia spp. cyanase hydratase

Components

Cyanate hydratase

Keywords

HYDROLASE / Enzyme / Lyase

Function / homology

Function and homology information

cyanate metabolic process / cyanase / cyanate hydratase activity / DNA binding
Similarity search - Function

Biological species

Serratia sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Pederzoli, R. / Tarantino, D. / Gourlay, L.J. / Chaves-Sanjuan, A. / Bolognesi, M.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Detecting the nature and solving the crystal structure of a contaminant protein from an opportunistic pathogen.
Authors: Pederzoli, R. / Tarantino, D. / Gourlay, L.J. / Chaves-Sanjuan, A. / Bolognesi, M.

History

Deposition	Jan 8, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 9, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Jan 24, 2024	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	6tv0.cif.gz	706.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6tv0.ent.gz	521 KB	Display	PDB format
PDBx/mmJSON format	6tv0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6tv0_validation.pdf.gz	13 MB	Display	wwPDB validaton report
Full document	6tv0_full_validation.pdf.gz	13 MB	Display
Data in XML	6tv0_validation.xml.gz	65.2 KB	Display
Data in CIF	6tv0_validation.cif.gz	90.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tv/6tv0 ftp://data.pdbj.org/pub/pdb/validation_reports/tv/6tv0	HTTPS FTP

-
Related structure data

Related structure data	4y42S S: Starting model for refinement
Similar structure data	1dwk-d 1dw9-d 2ivb-d 4y42-d 2iu7-d 2iuo-d 6b6m-1 2iv1-d 2ivg-d 7o74-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	#112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

-
Assembly

Deposited unit

A: Cyanate hydratase

B: Cyanate hydratase

C: Cyanate hydratase

D: Cyanate hydratase

E: Cyanate hydratase

F: Cyanate hydratase

G: Cyanate hydratase

H: Cyanate hydratase

I: Cyanate hydratase

J: Cyanate hydratase

hetero molecules

174 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	86.793, 93.140, 111.193
Angle α, β, γ (deg.)	90.000, 95.743, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

-
Components

#1: Protein	Cyanate hydratase / Cyanase / Cyanate hydrolase / Cyanate lyase Mass: 16931.391 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Serratia sp. (bacteria) References: UniProt: A0A4Q8D4S5, UniProt: A0A7G2JL56*PLUS, cyanase
#2: Chemical	ChemComp-OXD / OXALIC ACID Mass: 90.035 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₂O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 881 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.43 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 15% (w/v) polyethylene glycol 6000, 5% (v/v) glycerol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.95→71.64 Å / Num. obs: 91837 / % possible obs: 72.3 % / Redundancy: 6.6 % / B_iso Wilson estimate: 27.26 Å² / CC_1/2: 0.991 / R_pim(I) all: 0.089 / Net I/σ(I): 5.6
Reflection shell	Resolution: 1.95→2.17 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4590 / CC_1/2: 0.614 / R_pim(I) all: 0.56 / % possible all: 14

-
Processing

Software

Name	Version	Classification
REFMAC	1.17.1_3660	refinement
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Y42

4y42

Resolution: 1.96→71.64 Å / SU ML: 0.2252 / Cross valid method: FREE R-VALUE / Phase error: 24.6443

	R_factor	Num. reflection	% reflection
R_free	0.2185	4566	4.97 %
R_work	0.1763	-	-
obs	0.1784	91810	72.12 %

Solvent computation

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

Displacement parameters

B_iso mean: 38.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→71.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11930	0	330	881	13141

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	12435
X-RAY DIFFRACTION	f_angle_d	0.737	16800
X-RAY DIFFRACTION	f_chiral_restr	0.0449	1950
X-RAY DIFFRACTION	f_plane_restr	0.0042	2155
X-RAY DIFFRACTION	f_dihedral_angle_d	17.9494	4655

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 (%)
1.96-1.98	0.4628	2	0.3074	28	X-RAY DIFFRACTION	0.71
1.98-2	0.218	4	0.2583	90	X-RAY DIFFRACTION	2.28
2-2.03	0.2956	17	0.2439	189	X-RAY DIFFRACTION	4.87
2.03-2.05	0.3141	17	0.2457	417	X-RAY DIFFRACTION	10.36
2.05-2.08	0.273	25	0.2557	601	X-RAY DIFFRACTION	14.89
2.08-2.11	0.2447	34	0.244	857	X-RAY DIFFRACTION	21.01
2.11-2.14	0.264	43	0.2328	1050	X-RAY DIFFRACTION	26.01
2.14-2.17	0.2937	62	0.2327	1316	X-RAY DIFFRACTION	32.55
2.17-2.2	0.2513	80	0.2234	1566	X-RAY DIFFRACTION	39.44
2.2-2.24	0.2731	100	0.2282	2133	X-RAY DIFFRACTION	52.38
2.24-2.28	0.2629	154	0.2253	2865	X-RAY DIFFRACTION	71.61
2.28-2.32	0.2409	206	0.2244	3524	X-RAY DIFFRACTION	88.51
2.32-2.36	0.259	222	0.2135	3892	X-RAY DIFFRACTION	97.1
2.36-2.41	0.2426	206	0.2041	4013	X-RAY DIFFRACTION	99.95
2.41-2.46	0.245	223	0.1941	4033	X-RAY DIFFRACTION	100
2.46-2.52	0.2648	211	0.2015	3992	X-RAY DIFFRACTION	100
2.52-2.58	0.2559	235	0.2009	4029	X-RAY DIFFRACTION	100
2.58-2.65	0.2524	219	0.2003	3993	X-RAY DIFFRACTION	100
2.65-2.73	0.2381	230	0.2013	4029	X-RAY DIFFRACTION	100
2.73-2.82	0.2315	202	0.1921	4024	X-RAY DIFFRACTION	100
2.82-2.92	0.2175	201	0.1803	4025	X-RAY DIFFRACTION	100
2.92-3.04	0.2406	197	0.1668	4041	X-RAY DIFFRACTION	100
3.04-3.18	0.2217	218	0.1628	4044	X-RAY DIFFRACTION	100
3.18-3.34	0.1943	211	0.1498	4062	X-RAY DIFFRACTION	100
3.34-3.55	0.1925	226	0.1444	4007	X-RAY DIFFRACTION	99.98
3.55-3.83	0.1851	206	0.1481	4047	X-RAY DIFFRACTION	100
3.83-4.21	0.1721	192	0.1411	4068	X-RAY DIFFRACTION	100
4.21-4.82	0.1951	186	0.1492	4105	X-RAY DIFFRACTION	100
4.82-6.07	0.2221	222	0.1925	4066	X-RAY DIFFRACTION	100
6.07-71.64	0.2162	215	0.1968	4138	X-RAY DIFFRACTION	99.41

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	0.497631266751	-0.174634392628	-0.308370503135	0.810140433622	0.0204824696018	0.287893644813	0.0448360157937	0.0184118403154	-0.0830514132438	-0.113128601615	-0.0106575968184	-0.0527853508975	0.0317905905285	-0.0268439841427	-0.0216195864307	0.175281290715	0.000829527026213	-0.00669853368316	0.114729576717	0.0111892019048	0.19561836752	-12.2078773754	5.32926530794	-9.23984082995
2	1.24844151079	-1.73145959423	-0.0515272979968	2.449589894	0.0981711863466	-0.0164627942965	-0.0569677563954	-0.224390740757	0.0323669159513	0.132697278445	0.0294227524627	0.823703106135	0.0615804813511	0.102420269785	-0.0211839092944	0.239929034692	0.0281963071236	-0.0107006994672	0.163179798264	-0.0318354629906	0.262336397022	-16.176001687	14.6213062419	2.566149373
3	2.38974502996	-1.99127284014	0.740344837762	2.02910465066	-1.56546785937	2.77948604515	-0.0341782455643	0.0142633219835	0.341182924858	0.252286742675	-0.104458734687	0.0694217448262	-0.481273118055	0.27812209696	0.201349908307	0.247178985989	-0.0300897722523	0.0126836763884	0.138516101168	0.0240773336758	0.249231179138	-12.8400487935	20.8350635291	-1.07918228913
4	0.665642480521	-2.23977930423	-1.06809972529	9.44891131453	5.08018411539	2.8224555518	-0.284165843848	-0.0412367302787	-0.00142164655718	0.844367897721	0.254160254578	-0.226157264906	0.52404293064	0.0709079077425	0.032497743235	0.263891587887	-0.00233329251153	-0.000777827505636	0.187182540915	-0.011920328386	0.248954206967	-0.754736026309	-8.23746587355	-0.631297363365
5	3.8311627782	0.532223958146	0.716046526553	2.94268108092	0.864288290316	3.4602388393	-0.020534036913	0.475759354554	-0.158441385779	-0.0661687212627	0.00366320448551	-0.0530133417162	0.333049058207	0.417519031729	0.00350646029406	0.339648487045	-0.0374507385932	0.0771366785842	0.452400420915	0.127954554913	0.259382320538	1.04210659164	18.1998708132	-39.3069556819
6	1.80435631883	0.025662429971	-0.10213039077	0.880466895355	0.0174751412803	1.91691710747	-0.070729681416	0.281363019951	0.0672505335885	-0.237070725028	-0.000673484182057	-0.141210750249	-0.243725204916	0.295284584025	0.0456835935384	0.271526570195	-0.0583595844129	-0.00253078723054	0.202882094146	0.0416030860587	0.167717516754	-10.577698617	20.8917098617	-37.8582083558
7	2.24742310533	1.34501409041	1.49057478079	2.28299338241	0.939028640581	2.92836625185	-0.336253723248	0.27831674006	0.287371198491	-0.390215941819	0.10616700403	0.130600127861	-0.611099044692	0.0192271912543	0.263211401042	0.322517913541	0.0391211974336	-0.0529686934335	0.222986146005	0.0948072408284	0.266656022279	-23.4548420568	27.6571707359	-35.0639528574
8	1.13440801416	-0.358656866908	0.422114360297	5.03416369255	-3.3442744694	4.78456577957	-0.129128443205	0.32636690361	0.226576700748	0.280961807268	0.296690091004	-0.412468206978	-0.628801899298	-0.123026768662	-0.179649149203	0.28418113115	-0.0474682764697	0.039513326019	0.66776246035	-0.0438815889969	0.44987024995	-44.3710612166	-14.1756805337	-30.4172926165
9	2.59639923662	-0.567596206756	-0.807517126255	2.95440876738	-0.676192671664	4.9509358512	-0.0189846647302	0.290497671456	-0.617185396645	-0.273922807639	-0.158338511847	0.43032310962	0.554813508881	-0.597404357929	0.110693249395	0.260524737168	-0.101680399737	-0.0538655660549	0.353197257366	-0.0643864342365	0.351686108911	-42.9871309401	-27.9865785036	-34.8055822462
10	1.1309237594	-0.272081382618	0.362243746345	1.27565960709	-0.331027327876	2.25703692069	0.114223911765	0.0576811543694	-0.275508846514	-0.0607033821095	0.0620357590586	0.241310171139	0.0576130888029	-0.33948184224	-0.177260475262	0.214935716919	-0.0422488973204	-0.0356425663101	0.257557820669	-0.0501312656709	0.224823814125	-33.2992819211	-18.7302910477	-36.3717202647
11	0.58606701419	-0.174036865426	0.118452609535	0.826595654826	-1.50608309315	2.51226765078	-0.00899906057169	0.288084713413	-0.268449617607	-0.301695789659	0.23243345425	0.124275732069	0.276462100073	-0.164343097482	-0.18982438598	0.345338789225	-0.0173698218024	-0.0459974425951	0.393043412556	-0.163929821022	0.292543977193	-25.6930616737	-25.2217151815	-44.7848905826
12	1.76944204263	1.47154507484	-0.346812089617	5.35902795329	-3.99974487031	5.04106321939	-0.0418634725215	0.23147501035	-0.305140641357	-0.33045240709	0.103341595048	-0.149522868884	0.486895574394	-0.240780354588	-0.0228199329698	0.27010705088	0.0267892873311	0.0205176924344	0.292859856758	-0.165933818984	0.267829280924	-21.6670735199	-26.3528169172	-44.5266417352
13	2.85456713206	-0.207886664616	-1.64608435391	5.85871727107	0.291509553631	2.31395201272	-0.146798224358	-0.346191682882	-0.0479640728604	0.291864267915	0.123319172648	0.354113399688	-0.11931508189	-0.216090392891	0.0291894910113	0.227406626346	0.0640048992504	-0.0540675909895	0.499618864053	0.11891744788	0.321499035271	-48.8316833834	6.99334972776	-40.2898122754
14	0.89512259382	0.563232941367	0.200010117052	1.5857653987	0.0117747423789	0.21866164772	-0.167208941589	0.32410509172	-0.0807447107125	-0.282790233535	0.212228424365	0.034461677782	-0.118871797542	-0.0629397043996	-0.0407610694754	0.2892361462	-0.025079253459	-0.0411694016094	0.365153425547	-0.0155031185645	0.150271459449	-26.6617969451	4.34087834474	-47.7559900786
15	3.06451484085	2.52292107256	1.89613328276	5.07290091431	1.00023490358	2.07531674905	-0.484735891152	0.593375232458	0.129113170628	-0.889484965711	0.433247930994	0.378014539733	-0.168936653321	0.128916207973	0.0594350482577	0.356921391876	-0.0792521127696	-0.00875069299716	0.487317483887	0.0242623906486	0.172098170261	-26.4280265755	7.35409275127	-55.4882691927
16	3.21228535828	-1.56555444867	0.09379584097	3.5056095537	-0.731828411276	3.22038903214	-0.00724833051356	0.661404835387	0.0778280479183	-1.5162584479	-0.273445382	0.340450554025	0.289265072375	0.0103306377095	0.0366974196185	0.379372194042	-0.0784696637737	0.0595435831652	0.372156106402	-0.133218747793	0.567020692394	7.02111259693	9.90903842409	-22.6031382611
17	2.17782870663	-1.72258024006	-1.86087361183	2.09947122792	0.0581021130468	4.26815838354	-0.113332607835	-0.387657263387	-0.0140858045605	0.205183149229	0.046179331619	-0.637410731273	-0.0323252639531	0.472970628974	0.0667929175631	0.168313305081	-0.02967303567	-0.0213047737534	0.158344848423	-0.029961549375	0.315520286729	10.6538977993	13.2481479661	-7.34629172744
18	2.5435509523	-0.435455943516	0.401153693208	3.43409183091	-0.52662983214	2.82207670862	-0.0299017931462	0.337184465868	-0.0881369213021	-0.370794919955	0.110670366707	-0.516037297739	-0.291216292755	0.518883186281	-0.0637912174647	0.227827208962	-0.0753381483388	0.0587545592894	0.208645404139	-0.0388457392197	0.214125438697	9.46186883542	17.0708550631	-17.3675158252
19	1.31482372584	-0.0822755766661	-0.092696192457	0.626644809816	0.000560847390468	0.356887207374	0.00382182559243	0.0255754315883	-0.0285274500068	-0.0345531484202	0.0337771855454	-0.017981697521	-0.0313417568601	0.0319861232236	-0.0223214164752	0.196509744011	-0.0213433173127	-0.0153700263552	0.132000362665	0.00826994553503	0.175800613835	-12.5092519952	10.555998763	-9.29409053348
20	4.23464938742	-2.67414099073	3.18704193532	5.21815209808	-2.4615721427	4.04224456038	-0.27001819172	-0.167859325149	0.345717657741	0.534968011196	0.10750715128	-0.224050960647	-0.402404275772	-0.096622044703	0.125480218011	0.137807182066	0.00306291394449	0.0859949337845	0.140586019492	-0.0278814866389	0.121140417384	-13.6963588188	15.2002601502	-2.3590435791
21	3.94970990337	-0.257409157432	3.39811451608	1.98321425368	-0.435785536196	7.77347884622	0.349478822003	0.149814071098	-0.289590939836	-0.042374862532	-0.136977414623	-0.243062448911	0.997246948896	-0.00335734733019	-0.166315982175	0.302724553204	-0.0273750606033	0.0103519056194	0.420881278299	-0.0883346916433	0.554432066091	-40.9356416744	14.7795607672	-17.7541741271
22	1.59675982803	0.101178985428	-0.0553752726703	1.01982572055	0.0184201179116	1.81521193282	0.0149619414268	0.00104400666644	0.157364282118	-0.0663581830978	-0.0280729989108	0.267775473546	-0.307090902502	-0.355476891416	0.00644874471222	0.251403797723	0.0592103139955	-0.0425019056876	0.164459742196	0.0329097601285	0.234439900915	-30.452130083	22.4595310364	-22.7573345987
23	2.47268715551	-0.933568453271	2.03265560219	1.54000956439	-0.448632316891	3.39055296615	-0.124104060485	0.131745708042	0.512535643175	-0.320947387873	-0.0426680959338	0.181114300061	-0.488986042253	-0.180559574163	0.113803405236	0.410289537839	0.046712373171	-0.0407201966565	0.161617390139	0.117114726604	0.353571182433	-20.9140351284	29.7867608342	-29.3892717999
24	2.51052185898	0.138786525489	1.27825778071	3.13134753977	-1.95081604357	5.0497232568	-0.0894687912167	0.0234897225097	-0.055263181905	-0.0199598696051	-0.291599635697	-0.157267105353	-0.314457577312	0.349772387268	0.35505761049	0.257321770336	-0.023933393065	0.133548528162	0.610019779019	-0.183358825048	0.420671362076	1.24587228855	-19.0491040017	-41.6369061447
25	1.35860864265	0.24728237911	1.17089159835	3.4377984579	-0.727604727374	1.53287804413	0.130504420608	0.923471648462	-0.352515640814	-0.0637932758272	-0.189751437771	-0.2073359281	0.65726806934	0.885961754816	-0.0709153202802	0.345558094309	0.148602994447	0.0531828854263	0.534683013757	-0.270769781001	0.325884408115	-3.73042140471	-28.2046670941	-40.4769952875
26	3.42709998266	1.4102033484	-0.146673037492	2.84285968593	-1.46174826977	4.54890287302	-0.185113718881	0.737894450835	-1.1141028276	-0.752820529787	-0.506889555953	-0.326656545177	0.914252288119	0.41388777107	0.58173733216	0.398290474036	0.256006769852	0.026681151394	0.766089860889	-0.183172138561	0.508627444308	6.31749654501	-29.8543583093	-42.7479674551
27	4.87892654181	0.270192568862	-0.637105337242	5.91455619487	-0.236101077292	2.95861117112	0.207312684251	-0.146471112265	0.333648217471	-0.110873322483	0.158179630532	-0.965893891703	-0.0848600384807	0.696868250519	-0.32825257247	0.366083295996	0.132188934508	0.0053572590343	0.767530568941	-0.215608449985	0.398317759858	9.85078643354	-23.6344298694	-38.039299449
28	0.764867625573	-0.0577089881407	0.0587685958006	0.027748907697	0.10115526035	1.24848144528	0.0620230902612	0.194242802335	-0.232853184472	-0.0171710235906	0.0238858735583	-0.117589799331	0.012406207392	-0.0317195103616	-0.0925638230424	0.233243675546	0.00931163275967	-0.035255587407	0.27579117104	-0.118026090744	0.249369559265	-21.1427951321	-20.9044047486	-33.8589994115
29	1.35406296663	-0.312468716647	1.89226428527	0.0659051502407	-0.438252014454	2.61809778074	0.254595182608	0.41213693611	-0.405740550939	-0.149873196171	0.109950233963	0.241865856814	1.23587303597	0.481446757045	-0.250884375969	0.342561002826	0.0211482053205	0.00784546376278	0.403380567219	-0.159754209823	0.387057907895	-17.8241834344	-30.0457584534	-45.4027622621
30	2.16036045662	0.953465084343	0.91350349505	2.34863028891	-0.931983296281	1.91608997836	0.233405764858	0.513888705335	-0.316908432508	-0.803452233444	0.300211159292	0.809629139049	0.528796355917	0.531703692165	-0.336867845084	0.446169882978	0.0496752147776	-0.135405978472	0.349432858475	-0.130780681448	0.380909708973	-24.0274572512	-27.5484244343	-49.6941231846
31	0.319817732072	0.502597493853	1.46366347638	0.893877691576	2.40238280916	6.64171637484	0.161654370131	0.0625664512926	-0.254385176595	-0.00621417561276	0.237116316688	0.116095548874	1.1640590181	0.167487178266	-0.2885395791	0.338336779454	0.0230193896352	-0.0737344615847	0.162144725468	-0.0624734425711	0.3993037959	-24.4238738895	-33.0164838345	-18.873675228
32	1.69647057379	1.38091265431	-0.339167602009	8.74447193863	-1.95702935593	1.83336208916	-0.120419150525	0.143638982701	-0.232124417694	0.922938373635	0.345461064518	-0.62513836871	-0.328294685229	0.393416687334	-0.233245557938	0.419062068202	-0.0854330929351	0.0567290606053	0.81931122276	-0.237573427621	0.43743008555	-2.32884608473	-1.76276921319	-50.9498465394
33	3.78185872375	0.363515599572	2.2510052019	2.94437712549	2.82219514431	3.71760659082	-0.54467999988	0.250861352682	0.663335585147	-1.29781221878	0.181051422194	-0.210213031802	-0.638851141048	0.0403200742513	-0.0225086453113	0.629599633771	-0.213517368675	0.169873848003	0.791072016069	-0.078407724107	0.182089700869	-8.75865690372	4.54316362818	-64.3513901887
34	2.33503601526	-0.775926025818	-0.408493269938	2.45904555106	0.43210491871	1.32762924914	0.0750498897926	0.377768883505	0.0868819972592	-0.66316778636	-0.0155923514537	-0.565799626912	0.156950955079	0.292909466167	-0.0506872950629	0.426457345912	-0.0819970613423	0.138946262145	0.685764820768	-0.139678656032	0.303381697053	-4.43520325153	-4.35552156685	-59.4967168209
35	0.679862570802	-0.0154440286795	-0.128752794335	0.72059772766	-0.339653121385	0.576400947769	0.0136561058588	0.311555931399	-0.0740778445461	-0.0867917008567	0.114175253038	0.0587340991779	0.0219052110776	0.0346930962571	-0.131544397369	0.267936036503	-0.0131619927741	-0.0359940509277	0.339541842299	-0.0310375869346	0.187075914285	-26.6494096792	-0.473871861957	-46.3065899495
36	1.00206661689	0.204852688787	-0.0187665738711	4.07092954078	-1.91123931001	1.15482920205	-0.425090864894	0.766467992339	0.27088358877	-0.954794112458	0.336200350282	-0.0669795795667	-0.159940902059	0.40383283379	0.172813805716	0.618075658822	-0.230372845351	-0.0807215623843	0.810550323673	0.0698786354712	0.292129166029	-23.8518326331	5.58563771794	-60.0933964266
37	2.61381000118	2.82295189614	-0.128007198899	4.25789112578	0.852980097726	1.00325242275	-0.24887053133	0.463543994313	0.462749366487	-1.55769927732	0.0777905392186	0.868200299839	-0.458664317454	0.0808877551388	0.139240809129	0.555453775085	-0.0886158089193	-0.134621829978	0.590427316212	0.0943589477282	0.268720872589	-28.1056385251	12.1761903261	-58.0134806673
38	0.359811142713	-1.32265606884	0.905553712374	4.82679760541	-3.30801733013	2.26259428829	-0.17075233363	0.337441406479	-0.298679987982	-0.525780411645	0.430476011154	0.147753144793	0.546907152588	-0.216499640934	-0.278475842376	0.365215224432	-0.0221860877162	-0.0255057339756	0.499268488257	-0.0812231781542	0.279712794452	-35.7998503966	-17.215086285	-50.786059528
39	1.87357292589	-1.35662583427	-0.839630560961	8.63203735847	3.54544327885	2.21523235352	0.0571466033735	-0.0786794987355	0.225215841302	-0.998880842173	0.0950220091624	0.138200028232	-0.646812654706	0.490574075721	-0.1152555599	0.315724033774	-0.054879556146	-0.0037104310554	0.616696494375	0.0360820719171	0.286789086763	7.9722802624	-10.0519848133	-21.4202175234
40	2.32223755699	-0.506537358742	-0.461280332399	4.36822884324	3.54246471093	3.31509640551	-0.070994468136	0.272100800475	-0.891004814823	0.235819364311	-0.0490374846291	-0.112258861921	1.03502163653	0.277463024385	0.15694105467	0.234614755182	0.0541182208182	0.0162748981084	0.22254825608	-0.0406333653139	0.399620725678	9.60491925551	-23.8644647253	-13.2183806171
41	3.6752617135	0.039017092637	0.645214354133	3.15635962207	0.547515642915	3.72029728268	0.153803191716	0.478827932631	0.182126423196	-0.108116791643	-0.0269684107997	-0.703838681515	-0.168569081824	0.500816218274	-0.153519955199	0.183745299418	0.00561378776054	0.0221261669866	0.231004456373	0.0213045949128	0.311237000506	11.5892325009	-13.0790168933	-13.3328798889
42	1.38228710273	-0.00895099752202	0.295658684638	0.548054576866	0.278926538875	1.32553831826	0.0587877850875	0.131278942141	-0.127139382875	0.0530073796376	0.000393881355443	0.0218812219011	0.129953277165	0.111449798592	-0.0298118510192	0.173870754799	0.018143547567	-0.0130282070511	0.0900845537878	0.00759762027633	0.196083305772	-12.9510377158	-16.2165534927	-11.322165163
43	2.22162092497	-1.2109715868	-0.188949083766	5.9311654888	2.21994893322	3.24405989256	-0.0950993778552	-0.0483042116696	-0.136098270196	0.506867658806	0.244429688364	-0.0910980329447	0.498876966684	0.0533382509331	-0.110249965035	0.145776200332	-0.00174473931781	-0.00722659053002	0.105034560405	0.0408455513198	0.181523517209	-13.4491056624	-20.5558008444	-4.24524300748
44	4.18105157366	-0.55705070284	1.31806676504	5.24790642801	2.86330298322	3.50741534633	0.0400305152282	0.520892908593	0.398379430947	-0.510696325619	-0.266575676917	0.184595916984	-0.32688111079	0.00519033508504	0.214058016334	0.22984426957	-0.0228298881386	0.0716006580058	0.250390096466	0.133064342255	0.413346780491	-36.9433290646	-17.381438132	-8.57979795169
45	2.31571126488	0.308551755875	-0.104335375954	0.968327071475	0.221895450061	1.45405504972	0.0299502204705	0.0453102356525	-0.167727548113	0.0659440828027	-0.00941726512525	0.158651216333	0.127963737245	-0.209261646626	-0.0250688771751	0.181767883588	-0.0172942468298	-0.0181578924051	0.105722045734	0.0178853264866	0.191947339618	-25.9221884114	-20.7381130942	-11.2639229995
46	1.35094454531	-0.5032913064	-0.0788526043528	0.825213164495	-0.146666328286	3.59252686022	-0.0110353189767	0.0646285095438	-0.282665201912	0.0283654345418	0.0804744129271	0.0030113497344	0.253680910541	0.0378232882994	-0.0501645752835	0.194159681011	0.00440326411945	0.000981516801842	0.101548191238	-0.0275219539664	0.270509736841	-12.1359274864	-25.9917412603	-10.9291182615
47	3.10658973547	-2.68398433333	0.874238850499	9.56327847748	-0.987622114598	1.90650524442	0.266303207047	0.0670475618887	-0.597746071484	-1.05422971406	-0.118693531593	0.576389157844	0.221772536905	-0.124548494962	-0.0835367839028	0.287598020196	-0.00201857157829	-0.0312179597982	0.299275099417	-0.0431407138077	0.402434779631	-35.7140152679	1.01698799245	-4.7969739254
48	6.0101735942	-4.22119672516	0.97592323952	3.79126384089	-1.40125515023	0.819921485941	-0.240618515227	-0.704771369146	0.48678375414	0.904198791094	0.21883584671	0.141413712894	-0.61819190391	-0.189216535709	0.0838015787113	0.331087603789	0.0870513794227	0.126245881984	0.187846720824	-0.0538465919844	0.307423023974	-32.0101542102	12.2649631319	6.64320796757
49	3.67424578141	-0.495447651702	0.661642936	2.76214225472	0.00936457827721	2.59379202322	0.106014355873	-0.27832153669	-0.124408102649	0.463502884853	-0.111683228544	0.733046769025	-0.145590259849	-0.471510110478	-0.00572504210555	0.224552793858	0.0157474030402	0.0966116757963	0.187724063442	-0.0107558544994	0.292345866387	-33.9534445216	1.68653512899	4.73574121897

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'F' and (resid 77 through 125 )
2	X-RAY DIFFRACTION	2	chain 'F' and (resid 126 through 134 )
3	X-RAY DIFFRACTION	3	chain 'F' and (resid 135 through 148 )
4	X-RAY DIFFRACTION	4	chain 'F' and (resid 149 through 156 )
5	X-RAY DIFFRACTION	5	chain 'G' and (resid 2 through 32 )
6	X-RAY DIFFRACTION	6	chain 'G' and (resid 33 through 115 )
7	X-RAY DIFFRACTION	7	chain 'G' and (resid 116 through 156 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 2 through 24 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 25 through 47 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 48 through 115 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 116 through 134 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 135 through 156 )
13	X-RAY DIFFRACTION	13	chain 'I' and (resid 2 through 76 )
14	X-RAY DIFFRACTION	14	chain 'I' and (resid 77 through 134 )
15	X-RAY DIFFRACTION	15	chain 'I' and (resid 135 through 156 )
16	X-RAY DIFFRACTION	16	chain 'J' and (resid 2 through 25 )
17	X-RAY DIFFRACTION	17	chain 'J' and (resid 26 through 39 )
18	X-RAY DIFFRACTION	18	chain 'J' and (resid 40 through 75 )
19	X-RAY DIFFRACTION	19	chain 'J' and (resid 76 through 134 )
20	X-RAY DIFFRACTION	20	chain 'J' and (resid 135 through 156 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 2 through 24 )
22	X-RAY DIFFRACTION	22	chain 'A' and (resid 25 through 125 )
23	X-RAY DIFFRACTION	23	chain 'A' and (resid 126 through 156 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 2 through 32 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 33 through 54 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 55 through 65 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 66 through 75 )
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 76 through 125 )
29	X-RAY DIFFRACTION	29	chain 'B' and (resid 126 through 134 )
30	X-RAY DIFFRACTION	30	chain 'B' and (resid 135 through 148 )
31	X-RAY DIFFRACTION	31	chain 'B' and (resid 149 through 156 )
32	X-RAY DIFFRACTION	32	chain 'C' and (resid 2 through 25 )
33	X-RAY DIFFRACTION	33	chain 'C' and (resid 26 through 39 )
34	X-RAY DIFFRACTION	34	chain 'C' and (resid 40 through 76 )
35	X-RAY DIFFRACTION	35	chain 'C' and (resid 77 through 125 )
36	X-RAY DIFFRACTION	36	chain 'C' and (resid 126 through 134 )
37	X-RAY DIFFRACTION	37	chain 'C' and (resid 135 through 148 )
38	X-RAY DIFFRACTION	38	chain 'C' and (resid 149 through 156 )
39	X-RAY DIFFRACTION	39	chain 'D' and (resid 2 through 25 )
40	X-RAY DIFFRACTION	40	chain 'D' and (resid 26 through 39 )
41	X-RAY DIFFRACTION	41	chain 'D' and (resid 40 through 76 )
42	X-RAY DIFFRACTION	42	chain 'D' and (resid 77 through 134 )
43	X-RAY DIFFRACTION	43	chain 'D' and (resid 135 through 156 )
44	X-RAY DIFFRACTION	44	chain 'E' and (resid 2 through 32 )
45	X-RAY DIFFRACTION	45	chain 'E' and (resid 33 through 115 )
46	X-RAY DIFFRACTION	46	chain 'E' and (resid 116 through 156 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 2 through 24 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 25 through 39 )
49	X-RAY DIFFRACTION	49	chain 'F' and (resid 40 through 76 )

+
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://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