PDB-6hhb: Structure of iron bound IbpS from Dickeya dadantii

ID or keywords:

Entry

Database: PDB / ID: 6hhb

Title

Structure of iron bound IbpS from Dickeya dadantii

Components

ABC-type Fe3+ transport system, periplasmic component

Keywords

METAL BINDING PROTEIN / Substrate binding protein Bacterial effector venus fly-trap

Function / homology

Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACETATE ION / : / ABC-type Fe3+ transport system, periplasmic component

Function and homology information

Biological species

Dickeya dadantii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.80000342375 Å

Authors

Gueguen-Chaignon, V. / Condemine, G. / Terradot, L.

Citation

Journal: Nat Commun / Year: 2019
Title: A secreted metal-binding protein protects necrotrophic phytopathogens from reactive oxygen species.
Authors: Liu, L. / Gueguen-Chaignon, V. / Goncalves, I.R. / Rascle, C. / Rigault, M. / Dellagi, A. / Loisel, E. / Poussereau, N. / Rodrigue, A. / Terradot, L. / Condemine, G.

History

Deposition	Aug 27, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 19, 2020	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	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6hhb.cif.gz	682.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6hhb.ent.gz	464.8 KB	Display	PDB format
PDBx/mmJSON format	6hhb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6hhb_validation.pdf.gz	449.1 KB	Display	wwPDB validaton report
Full document	6hhb_full_validation.pdf.gz	453.4 KB	Display
Data in XML	6hhb_validation.xml.gz	57.4 KB	Display
Data in CIF	6hhb_validation.cif.gz	85.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hh/6hhb ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hhb	HTTPS FTP

-
Related structure data

Related structure data	6fjlSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hd6-d 1cb6-d 5e3t-1 6cn2-1 6p3k-d 6p59-2 3pmh-d 5edu-2 2c8j-d 5u3t-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 - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (2) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2)

Deposited unit

A: ABC-type Fe3+ transport system, periplasmic component

B: ABC-type Fe3+ transport system, periplasmic component

C: ABC-type Fe3+ transport system, periplasmic component

D: ABC-type Fe3+ transport system, periplasmic component

hetero molecules

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

1

A: ABC-type Fe3+ transport system, periplasmic component

C: ABC-type Fe3+ transport system, periplasmic component

hetero molecules

defined by author&software
Evidence: gel filtration, MALS
84 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ABC-type Fe3+ transport system, periplasmic component

D: ABC-type Fe3+ transport system, periplasmic component

hetero molecules

defined by author&software
83.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.891, 78.889, 83.913
Angle α, β, γ (deg.)	73.251, 74.741, 84.918
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1

#1: Protein	ABC-type Fe3+ transport system, periplasmic component Mass: 41885.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria) Strain: 3937 / Gene: Dda3937_02937 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SCP7
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1129 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.77 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 3350 0.1M BisTrisPropane pH 8.5 0.2M NaNO3

-
Data collection

Diffraction	Mean temperature: 173 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.589539 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 4, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.589539 Å / Relative weight: 1
Reflection	Resolution: 1.8→77.8 Å / Num. obs: 111675 / % possible obs: 86.4 % / Redundancy: 4 % / B_iso Wilson estimate: 22.1169963521 Å² / R_merge(I) obs: 0.05938 / R_rim(I) all: 0.06875 / Net I/σ(I): 10
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5326 / CC_1/2: 0.83 / R_rim(I) all: 0.6 / % possible all: 83.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6FJL

6fjl

Resolution: 1.80000342375→47.9914774494 Å / SU ML: 0.173448958097 / Cross valid method: FREE R-VALUE / σ(F): 1.9805155397 / Phase error: 19.9557844997

	R_factor	Num. reflection	% reflection
R_free	0.191143831402	5522	4.94581280788 %
R_work	0.155029073565	106128	-
obs	0.156820705143	111650	86.3395584426 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.8548546431 Å²

Refinement step

Cycle: LAST / Resolution: 1.80000342375→47.9914774494 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11004	0	16	1129	12149

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00783736213536	11340
X-RAY DIFFRACTION	f_angle_d	1.11028455336	15476
X-RAY DIFFRACTION	f_chiral_restr	0.0460748809093	1645
X-RAY DIFFRACTION	f_plane_restr	0.00563152447265	2017
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9266239073	4087

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 (%)
1.8-1.8205	0.289978341618	168	0.244020170224	3425	X-RAY DIFFRACTION	83.4029712163
1.8205-1.8419	0.254875983536	171	0.21242156543	3444	X-RAY DIFFRACTION	82.9889807163
1.8419-1.8643	0.247028219876	171	0.20474287988	3322	X-RAY DIFFRACTION	81.9953051643
1.8643-1.8879	0.249640543537	166	0.193448286513	3339	X-RAY DIFFRACTION	81.1718388143
1.8879-1.9128	0.256822747374	160	0.196450004542	3071	X-RAY DIFFRACTION	75.227008149
1.9128-1.939	0.255005662206	150	0.185786427818	3284	X-RAY DIFFRACTION	79.7121634169
1.939-1.9667	0.238017635512	197	0.182287426386	3554	X-RAY DIFFRACTION	86.7283236994
1.9667-1.996	0.250457929438	182	0.174971546816	3533	X-RAY DIFFRACTION	86.8599485621
1.996-2.0272	0.218961169907	179	0.18071841465	3630	X-RAY DIFFRACTION	87.2623138603
2.0272-2.0605	0.237829983004	187	0.17353311583	3512	X-RAY DIFFRACTION	86.5870786517
2.0605-2.096	0.232251135062	204	0.168071166064	3583	X-RAY DIFFRACTION	87.0174632353
2.096-2.1341	0.214373821302	188	0.155571520865	3467	X-RAY DIFFRACTION	85.3573096684
2.1341-2.1752	0.193494429862	197	0.155337445894	3508	X-RAY DIFFRACTION	86.0027855153
2.1752-2.2196	0.198473328078	150	0.15009860978	3426	X-RAY DIFFRACTION	83.3955223881
2.2196-2.2678	0.200017100363	172	0.156342663659	3260	X-RAY DIFFRACTION	78.9146930329
2.2678-2.3206	0.200009423702	184	0.158438794813	3239	X-RAY DIFFRACTION	80.107652703
2.3206-2.3786	0.211375325314	195	0.156695697782	3775	X-RAY DIFFRACTION	90.7428571429
2.3786-2.4429	0.181477777572	206	0.160379069789	3662	X-RAY DIFFRACTION	90.7342247244
2.4429-2.5148	0.211036110849	179	0.163301381716	3699	X-RAY DIFFRACTION	90.4384328358
2.5148-2.596	0.198247962124	202	0.16081889685	3687	X-RAY DIFFRACTION	89.7323488694
2.596-2.6887	0.203163454101	184	0.161113390623	3715	X-RAY DIFFRACTION	90.2546296296
2.6887-2.7964	0.184663886368	208	0.169179474034	3607	X-RAY DIFFRACTION	88.7415678065
2.7964-2.9236	0.202356231339	198	0.17897404003	3530	X-RAY DIFFRACTION	86.3762743281
2.9236-3.0777	0.247479495021	168	0.181653500684	3237	X-RAY DIFFRACTION	79.2597765363
3.0777-3.2705	0.20644767068	194	0.176720990421	3719	X-RAY DIFFRACTION	89.8507462687
3.2705-3.523	0.201116814659	195	0.161280814386	3811	X-RAY DIFFRACTION	93.6856875585
3.523-3.8774	0.186764594932	183	0.137529471477	3873	X-RAY DIFFRACTION	93.9541348158
3.8774-4.4381	0.145172779184	195	0.120624398877	3796	X-RAY DIFFRACTION	92.5341989335
4.4381-5.5902	0.124583488381	195	0.112192110921	3521	X-RAY DIFFRACTION	86.4186046512
5.5902-48.0085	0.130515598447	194	0.124904472313	3899	X-RAY DIFFRACTION	94.8551564311

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	0.377605904972	0.0385892526903	-0.079588429272	0.206604176424	0.0174957025407	0.279072766716	0.148983955356	0.358575194178	0.132635030204	-0.279412654853	-0.0683911774063	0.302874536667	-0.47132489633	-0.570430518374	-0.00101218635173	0.329327573024	0.125359967916	-0.00918936922067	0.317566641183	0.0405526554076	0.384519051223	-17.4669010702	23.6298211499	-16.477596394
2	0.690159174626	0.316785576433	0.0999930795494	1.22209081857	-0.137493389566	1.23480107019	-0.0311690128725	-0.0261189385396	0.059142058217	-0.00529521477951	0.0318971736943	0.161277912556	-0.122463013039	-0.0396047333998	-0.000471974778657	0.178811759385	0.033699013638	3.21593714782E-5	0.191836038903	-0.0117096422891	0.213631992169	-8.13148895149	10.8181362155	-8.44858560691
3	0.560613040513	-0.0224158829699	-0.490011744642	0.425547493765	-0.0746441731867	0.458319357213	-0.118490534572	0.0603787930971	0.037805853352	-0.0575297943495	0.0840813503206	-0.0672063930371	-0.364501956802	0.0762329222704	-8.2084616112E-5	0.239318668689	0.00433371515831	-0.019801814613	0.150970657288	0.00231892013421	0.186069572799	8.02543550889	15.3519784434	-7.53296220136
4	0.58242542709	0.133643107659	-0.279145667269	0.741071660595	0.255554668729	0.722763943852	0.00523353444388	-0.0183181208322	-0.116062343659	0.0807880888384	0.0102526049986	-0.32683291756	-0.0550114615585	0.162430968833	0.000896270401412	0.19451028816	-0.00578601328294	-0.0379640686451	0.205626027023	4.00760515743E-5	0.271634191609	21.4396947773	5.38858495212	-1.03170533091
5	0.402191804176	0.303224838191	0.25791649216	0.219846180252	0.199561005048	0.702613421464	0.000632777821269	-0.120282186702	-0.0581430359576	0.11310720428	-0.00197737993396	-0.164061224279	-0.210397254395	-0.00666277001911	-0.00141136354148	0.260460563395	-0.0112304792405	-0.0459742306614	0.197741898954	-0.00965550131612	0.19342188661	13.2802327284	13.122383313	5.703072333
6	0.372320399264	-0.681611377546	0.0845648969361	1.22067321232	-0.146336635837	1.17005583539	-0.0121730831269	-0.111266241214	-0.0760746161574	0.022321389335	0.0234682932209	-0.0182500046286	-0.110748974927	0.0193993024447	-0.000878509867306	0.178643688328	0.0231434897008	0.0239181970105	0.16796216695	-0.00882520585899	0.138883890979	4.51722200385	13.0484312802	-8.90926863134
7	0.552217697	0.0719220263734	0.199440406478	1.01874798928	-0.179959827872	0.434176864743	-0.0072681403201	-0.00681660594932	-0.00305931500008	-0.0233443849704	0.00100080911314	0.0336555294948	-0.088701265873	-0.0178617827388	1.16012827686E-5	0.188234481884	0.00837777436182	0.00466040896385	0.160775613952	-0.00787283884735	0.129042357041	3.2912287578	10.8216867946	-8.14203344328
8	0.361082294305	-0.0240370770044	-0.0307592726382	0.0902644015342	0.0242603816308	0.171440319102	0.0107883666451	-0.127245573403	0.0778454504357	0.540466658634	-0.107298118191	0.432974035434	0.192378957627	-0.463818701599	-0.0007421900665	0.345004100088	-0.0567291447546	0.0154156903022	0.319704381832	0.0432563763589	0.336085917454	-0.993968515772	-17.2543673327	47.3529477255
9	0.831912587935	-0.107408129975	-0.0384637581255	1.39519917909	-0.22994731035	0.84586995292	-0.00707347965661	0.0574161851105	-0.00775341073787	0.0129250185671	0.0295127243632	0.121728833246	0.0856903199074	-0.0700677962815	-6.62554622933E-5	0.173370496444	-0.0186421104041	0.00443448746587	0.199832010917	0.00607061429952	0.170542435588	10.1428343446	-6.08693423944	38.996731878
10	0.339434850515	-0.121664913237	0.107628387475	0.387341891069	-0.296474572713	0.225044296207	-0.027765731799	0.0278295441985	-0.0747934284356	-0.0507540618231	-0.0285917596367	-0.0885219504672	0.086853686928	-0.0358759255607	0.000125170849838	0.238203112006	-0.00238107215646	0.0233445286838	0.210235963502	-0.003479634422	0.186469450248	25.0068585903	-13.4434247163	37.452685335
11	0.528238624817	-0.00233104604018	0.0966997705679	0.67153166175	0.10900006098	0.923459905657	-0.10248487493	-0.022115270156	-0.0764496349011	-0.012392704162	0.0586721242416	-0.310946155138	0.14123733263	0.216058646481	-0.00121702214946	0.24003152514	0.011312476675	0.0420899168041	0.235987626092	-0.00321064053168	0.298468159483	39.8525861749	-5.96725719926	30.5646394935
12	0.281196348244	-0.121164820287	-0.00655555451902	0.164487329847	0.124570513675	0.722054409064	-0.0618647829557	0.0669375082598	-0.00822512724987	-0.103036612776	0.0499207764722	-0.052747840165	0.156244177961	-0.0425223031459	-1.03295943567E-5	0.262109087657	-0.00263802150575	0.0382192239512	0.202800517351	-0.0284573694417	0.201429540666	30.3682612141	-11.8436130575	23.992112054
13	0.586806009964	0.756892030087	-0.193929028323	1.14255438674	-0.503752481261	0.980707575089	0.00707870682154	0.121916546469	-0.0456547791353	-0.0463739870293	-0.0262737149227	-0.0505716154996	0.070408545757	0.00945877024033	-0.00116679994546	0.214887415401	-0.00461098938198	-0.0127404953237	0.198314249025	-0.00455668252066	0.125301078685	22.1013503066	-10.5168177444	38.960738311
14	0.554648009315	0.0394501017881	-0.0955551073981	0.652944029322	0.0653364992081	0.506735067469	-0.0149638329977	0.00417970809131	-0.0465166715944	0.110109595919	0.0185094980279	-0.0309008060852	0.120833128229	0.00982414326924	-6.94493545239E-7	0.242297430948	-0.00604744951486	-3.05358043095E-5	0.185789908357	0.00934525914459	0.154186938428	20.5159294477	-15.6971204267	43.7149726229
15	0.29167126039	0.218060119439	-0.361039297747	0.73198040688	-0.0565519998986	0.506956834665	-0.0590954464401	0.122096905821	0.191447656456	-0.0887319209796	0.0659176665192	0.00440651196808	-0.0423210142364	-0.0744061726035	-1.8910990641E-6	0.218624414919	0.0177597607268	-0.00899293163063	0.200064687712	0.020256305036	0.188397268937	22.7924866552	4.64468564729	29.3602029004
16	0.658751449637	0.275318781959	0.0253953750268	0.750710475625	-0.649718411326	0.703959193022	-0.0733018292457	0.0800548590524	-0.277139180427	-0.53783787411	-0.126587711949	-0.500483061307	0.614440135635	0.599284505822	-0.165480679644	0.327629056797	0.123487947618	0.0146418199616	0.366246162951	0.00420460062393	0.482558597842	24.6215419765	-41.3524042927	-10.9291802575
17	0.149010758703	0.0450443695478	0.0131774016156	0.284072648864	0.267473919213	0.249219386737	-0.0522964374574	-0.178331230555	-0.189074635782	0.244672882187	0.157615146841	-0.0999591880127	0.292725719062	-0.0738300644824	0.000739103092149	0.229293208487	0.0344214570466	-0.0289382869093	0.267463257723	0.0538944060665	0.291210488602	15.8390716628	-32.4328885251	3.56908188616
18	0.501713244778	0.242181529417	0.122577082684	0.240170665444	0.0151435196381	0.385802380526	0.0870464092494	-0.145708874201	-0.03204857672	0.0503912809	-0.0554628823818	-0.261864618528	0.0246484429179	0.119702481927	0.00219661389329	0.185174856978	0.0319954488275	-0.0311486477351	0.224568318151	-0.00583659940042	0.260091023225	17.755626493	-22.2958929294	-0.939776070725
19	0.181816069332	-0.0216347594402	0.0781113072301	0.420450516436	0.116016842011	0.152403150658	-0.0553238129995	0.0469807476093	0.0114137311632	-0.190965050838	0.0132297968242	-0.264943576949	-0.0524556583833	0.0797825876243	-2.20036457764E-5	0.205350236632	0.0235213971658	0.00680946623066	0.212576579231	-0.00214585328418	0.284437044904	15.577493638	-21.1010690742	-10.0064088557
20	0.0948636522035	0.0814825121109	-0.00124041748087	0.13054672811	0.0252193184484	0.318329287439	-0.0439163555324	0.148468577601	0.011566205413	-0.186556534643	0.0394299374569	-0.0503110267115	0.187651922415	0.0347530902438	-0.000120459864994	0.270518116944	0.0469919613175	0.0279081113315	0.219387785498	-0.00470254037276	0.246432429992	12.1240431031	-34.4871392935	-16.2896035116
21	0.513552047921	0.0680367171142	0.266905073259	0.622229975571	0.173020940534	0.226195068752	-0.111969547383	0.0274250677431	-0.258579432817	0.0148436124639	0.00969819780739	3.09513973119E-5	0.275454742381	-0.0963932553156	-0.000108810104035	0.229065428016	0.00706485396655	0.00855561497298	0.207308970671	0.0171089582219	0.22725355334	-0.364302136557	-31.3316999546	-2.3504967401
22	0.447394774893	-0.363376477523	-0.0850388639702	0.334977727667	0.193567436737	0.377978391425	-0.0416256289834	-0.226623610718	-0.254284429006	0.14409980224	-0.0468143676608	0.205796380096	0.12657002123	-0.11070410025	3.39394347131E-6	0.2465641599	-0.0036050171037	0.0495595748205	0.247511470664	0.0146676142617	0.281084972452	-13.9536495772	-23.5775619298	6.91679146062
23	0.857034511238	0.354943708959	-0.0874110527828	1.07833688331	0.127960128743	0.614692006251	0.0366946615068	-0.193583342845	-0.040784621431	0.188375641513	-0.00710082986212	0.205528381005	-0.0520801578601	-0.0738584698381	0.00011258068269	0.203268204192	0.00174164935565	0.0420049270531	0.233557749459	0.0179149432481	0.209518638339	-9.50800786336	-19.2969271122	4.17565620231
24	0.102619848189	-0.143535047092	-0.0910347001983	0.237792241363	0.193213129428	0.188100875727	-0.137066899128	-0.414851739692	-0.257565330454	0.27234878147	0.200028386825	0.259768552944	0.210986410616	-0.301529079241	0.00399040072474	0.26632993475	0.0238782280431	0.018211884794	0.295330099902	0.070370881642	0.249990650958	-8.6363722981	-34.6673875252	3.1459765368
25	0.795176666458	-0.291054457003	0.0306350249604	1.1282167399	0.148846736722	0.723067063439	0.0274054173144	-0.0844104131756	-0.134441157689	-0.0792192040978	-0.0452167110607	-0.0456579572001	0.143245413004	0.0260535204676	4.37058099553E-5	0.210301838101	0.0221616132264	-0.00987828228283	0.185347796899	0.00368250258356	0.206629843819	6.00441615032	-33.7446009062	-8.10388910188
26	0.154191428171	-0.0306938365304	-0.238943663557	0.611364892903	-0.129967810709	0.389968901114	-0.0496203543524	-0.0744718058149	0.0761914472983	0.158589904221	-0.00138112500217	-0.0805561914369	-0.0809089036871	0.106228923065	-7.00680325649E-5	0.18721501977	-0.0112358466648	-0.0135588419196	0.199157708592	-0.0134942673841	0.207246721152	5.20515903046	-12.6501291554	1.94985153135
27	0.635096782634	-0.673853325601	-0.320446013714	1.92124672526	-0.439292135998	0.681452127361	-0.221095954712	0.183401026409	0.306312454202	0.190796015014	0.244549563874	-0.582107938251	-0.354743221934	0.58575568253	-0.0681338014107	0.323127512004	-0.181849814642	0.00559600873983	0.540344109966	-0.0695981646173	0.393687962711	51.9316896567	39.2159666226	40.7375894128
28	1.06037029134	-0.0871397506862	-0.0517021905198	1.42951304838	-0.0402858220963	1.17939799598	0.00758997510333	0.0382845350068	-0.00456717735287	-0.0143362085378	0.0547089387402	-0.231717028449	-0.125463252714	0.13399442028	0.00195094029486	0.16921381219	-0.030866889675	0.0135420213183	0.217320426933	-0.00260886254457	0.190936816443	40.1718559099	27.0658619747	35.2025283884
29	0.428813593833	0.152346292318	-0.235461131654	0.445721653637	0.0161775060608	0.245379059076	-0.184657770013	-0.105329400835	0.128445377803	0.00185252588026	0.119351541722	-0.0197112611669	-0.388322810672	-0.0941470209768	0.000200331787806	0.272494473598	-0.00963869243585	-0.0176031536246	0.184141925022	-0.00625356373015	0.172005734057	25.1788577757	34.131492271	32.7618137176
30	0.756470437316	0.226492498821	-0.231080498092	0.783085442698	-0.0977136243644	0.993746267808	-0.0233229507207	0.00404062139453	0.0266577713174	-0.073803330598	0.0925228629845	0.304546535141	-0.0872745363524	-0.193496083578	-7.04288686783E-5	0.22037968382	-0.0168699032185	-0.0280229994723	0.237715094133	0.0261230537476	0.222136838908	10.0241063309	25.6882433032	28.0747846956
31	0.481811849903	-0.330211954149	0.312919319192	0.401878298602	0.12698237998	0.781557677496	0.0162205079478	0.110742649373	-0.00981005729327	-0.203032709345	0.0742193539738	0.0694978526286	-0.195825115497	0.109909566105	0.000166925279081	0.275859132223	-0.0307804542629	-0.0132415795259	0.245514683527	0.020823933584	0.173704933081	19.3443370112	30.0972039049	20.2404367642
32	0.497170950568	0.800222799174	-0.0940380508487	1.33571387015	-0.0374981599976	1.37123568725	0.0732834485721	0.120026453075	0.0151171354743	-0.0733424208363	-0.00985002555993	-0.0150795181615	-0.103388032346	0.0637934897771	-0.00123135915035	0.202693905753	-0.0229330869659	0.0275273181875	0.174210686475	-0.0262184082374	0.119474853694	28.1966739331	31.4772252061	34.7536402517
33	0.203234337051	0.00936212771641	0.207822568234	0.683110472709	0.240703291768	0.586093157023	0.0109913586385	0.0331320051044	0.078263390902	0.00309225212354	-0.0200127089782	-0.108123361756	-0.222400999747	0.0979739062011	7.7710534291E-6	0.240807814617	-0.0259321682515	0.00302653125734	0.21834267998	-0.00991339559801	0.19035601158	30.0461343503	37.4534572546	38.3288373918
34	0.168827962183	-0.00367528283034	0.241421449872	0.669602769637	-0.227153480268	0.415493557786	-0.0514428981319	0.0260983762375	-0.106650636236	-0.130923308706	0.0696304621647	-0.0532050253823	0.112249573696	0.100823797663	-3.22872918715E-5	0.2383199108	0.00254808247617	0.00875874208415	0.234778335572	-0.025158587528	0.20760188418	27.1436029575	14.7489453266	28.3353790008

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 47 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 139 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 140 through 164 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 165 through 217 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 218 through 253 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 254 through 280 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 281 through 372 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 47 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 48 through 139 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 140 through 164 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 165 through 217 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 218 through 253 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 254 through 280 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 281 through 336 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 337 through 372 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 28 through 47 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 48 through 73 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 74 through 99 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 100 through 121 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 122 through 139 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 140 through 164 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 165 through 192 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 193 through 243 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 244 through 265 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 266 through 336 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 337 through 372 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 28 through 47 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 48 through 139 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 140 through 164 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 165 through 217 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 218 through 253 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 254 through 280 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 281 through 336 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 337 through 372 )

-
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