PDB-5zmy: Crystal structure of a cis-epoxysuccinate hydrolase producing D(-...

ID or keywords:

Entry

Database: PDB / ID: 5zmy

Title

Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)-tartaric acids

Components

Cis-epoxysuccinate hydrolase

Keywords

HYDROLASE / Zn-binding / TIM-barrel

Function / homology

3-keto-5-aminohexanoate cleavage activity / 3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase-type TIM barrel / hydrolase activity / metal ion binding / D(-)-TARTARIC ACID / Cis-epoxysuccinate hydrolase

Function and homology information

Biological species

Bordetella sp. BK-52 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Dong, S. / Liu, X. / Wang, X. / Feng, Y.

Funding support

China, 1items

Citation

Journal: Chem. Commun. (Camb.) / Year: 2018
Title: Structural insight into the catalytic mechanism of a cis-epoxysuccinate hydrolase producing enantiomerically pure d(-)-tartaric acid.
Authors: Dong, S. / Liu, X. / Cui, G.Z. / Cui, Q. / Wang, X. / Feng, Y.

History

Deposition	Apr 6, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5zmy.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb5zmy.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5zmy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/5zmy ftp://data.pdbj.org/pub/pdb/validation_reports/zm/5zmy	HTTPS FTP

-
Related structure data

Related structure data	5zmuSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5zmu-1 6trv-d 3no5-2 5brb-d 3no5-1 6dq3-d 4fc5-9 5zm2-1 1r2s-2 3u02-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5zmuSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: Cis-epoxysuccinate hydrolase

B: Cis-epoxysuccinate hydrolase

C: Cis-epoxysuccinate hydrolase

D: Cis-epoxysuccinate hydrolase

E: Cis-epoxysuccinate hydrolase

F: Cis-epoxysuccinate hydrolase

G: Cis-epoxysuccinate hydrolase

H: Cis-epoxysuccinate hydrolase

hetero molecules

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

1

A: Cis-epoxysuccinate hydrolase

B: Cis-epoxysuccinate hydrolase

hetero molecules

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

2

C: Cis-epoxysuccinate hydrolase

D: Cis-epoxysuccinate hydrolase

hetero molecules

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

3

E: Cis-epoxysuccinate hydrolase

F: Cis-epoxysuccinate hydrolase

hetero molecules

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

4

G: Cis-epoxysuccinate hydrolase

H: Cis-epoxysuccinate hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	135.159, 158.348, 134.090
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	Cis-epoxysuccinate hydrolase Mass: 34648.129 Da / Num. of mol.: 8 / Mutation: D115A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella sp. BK-52 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F1LJ99
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2563 / 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: 2.59 Å³/Da / Density % sol: 57.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.1 M magnesium formate dihydrate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 1.87→158.35 Å / Num. obs: 234863 / % possible obs: 99.9 % / Redundancy: 7.3 % / B_iso Wilson estimate: 20.25 Å² / R_merge(I) obs: 0.128 / Net I/σ(I): 9.9
Reflection shell	Resolution: 1.87→1.92 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.608 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 17249 / % possible all: 100

-
Processing

Software

Name	Version	Classification
XDS		data reduction
PHASER		phasing
PHENIX	1.13_2998	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ZMU

5zmu

Resolution: 1.87→49.11 Å / SU ML: 0.138 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2613

	R_factor	Num. reflection	% reflection
R_free	0.1947	1996	0.85 %
R_work	0.1678	-	-
obs	0.168	234588	99.82 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→49.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17395	0	88	2563	20046

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	18232
X-RAY DIFFRACTION	f_angle_d	1.0964	24822
X-RAY DIFFRACTION	f_chiral_restr	0.0657	2714
X-RAY DIFFRACTION	f_plane_restr	0.008	3319
X-RAY DIFFRACTION	f_dihedral_angle_d	9.7957	10932

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 (%)
1.87-1.92	0.2344	143	0.2063	16486	X-RAY DIFFRACTION	99.98
1.92-1.97	0.2322	141	0.1934	16466	X-RAY DIFFRACTION	99.98
1.97-2.03	0.2099	148	0.1807	16549	X-RAY DIFFRACTION	99.96
2.03-2.1	0.2167	137	0.1769	16489	X-RAY DIFFRACTION	99.93
2.1-2.17	0.2018	141	0.1753	16516	X-RAY DIFFRACTION	99.93
2.17-2.26	0.1997	141	0.1678	16491	X-RAY DIFFRACTION	99.86
2.26-2.36	0.1851	141	0.1627	16572	X-RAY DIFFRACTION	99.95
2.36-2.49	0.2123	139	0.1619	16578	X-RAY DIFFRACTION	99.95
2.49-2.64	0.1718	146	0.1579	16596	X-RAY DIFFRACTION	99.94
2.64-2.85	0.2095	143	0.1646	16626	X-RAY DIFFRACTION	99.96
2.85-3.13	0.1782	146	0.1598	16633	X-RAY DIFFRACTION	99.93
3.13-3.58	0.1829	145	0.1568	16733	X-RAY DIFFRACTION	99.9
3.58-4.52	0.1822	146	0.1456	16816	X-RAY DIFFRACTION	99.84
4.52-49.13	0.1987	139	0.1966	17041	X-RAY DIFFRACTION	98.48

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	1.55821944075	-0.510110190073	-0.250278373151	2.52832090461	0.0197816602368	2.38303401116	0.0657747159158	0.0167786264059	0.198979802499	-0.0555439554396	-0.0602421636254	0.0335739928236	-0.321942931921	-0.0228918008024	-0.00320505399681	0.107939135161	-0.0140149514961	0.0107110776864	0.083380066742	-0.0182376670397	0.167036434902	-58.2405735806	24.1277388127	-43.9591778623
2	2.0892865289	0.142582988096	0.186253039307	0.924283658926	-0.207608699159	0.578956737226	-0.0535019621562	0.0363255212376	0.273748428444	0.0199809833718	-0.0215942701926	0.0525578931429	-0.160743771055	0.00385902988275	0.0494769603156	0.146920660512	-0.0192647069613	-0.0130678266958	0.130080670695	-0.0173320257131	0.191920775823	-41.9486658709	23.4952937834	-32.952952519
3	0.788089677971	-0.100419710056	0.549313111339	0.725950620927	0.190443022344	1.51395671349	0.0214895023981	-0.0356277452612	-0.00345504874113	0.0200604268384	-0.0428373402316	0.0461168085435	-0.00479134517315	0.0330545387093	0.0187305047937	0.0714457589631	-0.0180200568982	0.0262307925859	0.0816994982928	-0.0117049128398	0.146345407972	-49.00063165	9.41960261893	-38.4360466882
4	2.29374065312	0.177049719076	-0.778019678519	2.60936794169	0.819589918267	2.94398161288	-0.0215668124818	-0.0577024811107	0.145573111746	0.0728751746814	0.0296218647544	-0.109059427422	-0.171005884907	0.15245184199	-0.001846967115	0.0814634057948	-0.0372737739941	-0.0164855405657	0.124985895049	0.0119272427431	0.141950562265	-12.3998170742	21.3362956133	-16.123157354
5	0.753823231425	-1.19511760591	0.477258287971	2.90236258435	-1.58305385098	3.20522390394	-0.0888285778658	0.0451803419304	0.18127083061	0.0221045356022	-0.0630671280678	-0.0589673107089	-0.303581906275	0.161494624833	0.144176277804	0.119889287696	-0.0610808214994	-0.0140275397397	0.162429864925	0.00799082446562	0.250308153887	-5.31404116274	28.8060792178	-25.0927452906
6	3.54363430233	0.580942446044	-1.29005374148	0.967646758309	-0.770293681832	0.876847446957	0.106871785484	-0.598451979337	0.252072699412	0.161655242021	-0.0502319337449	0.0267413492117	-0.267450810984	0.156329623027	-0.0552092016842	0.167148553313	-0.0284700960576	-0.0212559107193	0.206310662381	-0.0596237717403	0.157944082422	-31.599373044	22.6362945452	-20.9340696648
7	3.98350572753	0.927476140427	-1.52267902196	0.592867977103	-0.635075356096	0.789595517276	0.139423578923	-0.0504748133424	0.483888660784	0.017128358676	-0.0409501668286	0.0529507393791	-0.272159025079	0.163352018667	-0.129480799776	0.197268865189	-0.0356248481069	-0.0286120207139	0.170197040852	0.00246508481301	0.256791010987	-23.8915121265	28.5267071512	-32.8710160475
8	2.56590088348	0.424552046828	-0.667582234332	0.717264448352	-0.454942297281	2.42929827285	-0.0570079117511	0.0952246361319	-0.0549062690682	-0.0881381492727	-0.0347885797865	-0.042340805613	0.0435744307982	0.053188238922	0.0814021191345	0.0901498255843	-0.0263286965921	0.00298466577995	0.0989816746252	-0.00558691322682	0.144091648987	-24.3184909621	14.0452346657	-33.4004706965
9	0.139925330409	-0.174927402725	0.00462767113866	0.605098454577	0.711701417701	1.85394164101	-0.0523560228046	-0.00946189669602	0.0129854226088	0.00923118884706	0.00847105993785	0.00244624329587	0.00555939596653	0.0504691964189	0.0490602312716	0.0878554417641	-0.0283728026486	0.0104936696331	0.124213388509	-0.000992014004839	0.183536744008	-19.7005264397	9.86445934851	-19.530139654
10	0.46598140626	0.534888509635	1.07481929007	3.33754796513	5.35175827491	8.6973449562	0.0160222373116	-0.159530642443	-0.155178488041	0.264807913293	0.306650158359	-0.609210900432	0.123956952935	0.357887075819	-0.300627498742	0.0857389322658	-0.00870961859806	-0.0159096897094	0.151888499692	0.0138739629023	0.20889350874	-11.9390070898	5.05882827053	-15.6491120688
11	1.8797552014	-0.473956125908	0.631798903885	0.865546597868	-1.01764822218	1.19602174042	-0.15913514761	-0.00700981866325	-0.214997628444	-0.235280067473	-0.241840745031	-0.624430599726	0.10457318724	0.327231356846	0.401146759016	0.120772345443	0.00617602259254	0.0555577539893	0.183426569636	-0.00141982695821	0.290755017973	-6.01766068033	7.46912318294	-29.1906202523
12	3.94099464085	-2.55156085912	-1.1913243753	3.34506047426	0.8528738864	2.02021320881	0.0430974377782	-0.154896799844	-0.0482033556957	0.082825051726	-0.00151378447451	-0.103356270769	0.0911698175028	0.00644519329947	-0.0367889751463	0.088303160816	-0.0661427314603	-0.00137386466467	0.103437498105	0.0187482013574	0.147797694461	-16.6728705184	-18.7727758781	-9.94476104635
13	3.00980217858	0.362208103469	-0.430695589502	3.26167098959	-0.404208374859	1.36898918703	0.0358689321853	-0.0691391982745	-0.309362679168	0.0619910244938	-0.0763765283612	0.0137476128929	0.458940971049	-0.221040330299	0.0440556679608	0.236265223558	-0.0844816747017	-0.0112774008201	0.161738594793	0.0126907585063	0.169442538191	-24.1429328433	-28.9181584214	-6.02444849306
14	0.314570067807	-0.396935802686	0.193577818346	1.25386977356	0.746982641716	1.44798377803	0.0649174402595	0.161924029812	-0.323701713482	0.110078704987	-0.177675005143	-0.0887774492695	0.45741806652	0.00787767908805	0.127213249162	0.159477675178	0.000778965320128	-0.0207523736304	0.276578742466	-0.0120787752205	0.254013071065	-29.4125480354	-27.00174132	-24.8840230799
15	0.83232229961	0.228464305227	0.43756093457	0.91030131869	0.173167385803	1.05486329313	0.0732045521769	0.00892196949195	0.00708955112547	0.00582209956064	-0.0732483835674	0.03059286819	0.0541681972145	-0.14354785361	-0.0052097234874	0.0725346628356	-0.0152196214239	0.0146475338528	0.132436641661	-0.00685084029206	0.14671083157	-29.9391073456	-13.173851398	-20.5006537572
16	9.26253555155	-6.86951602079	1.5060930541	5.10481676151	-1.22699130732	1.11332935096	0.0593004010207	-0.0312736137012	0.355839974602	0.238321977534	-0.174334656593	-0.4088510992	-0.0887512750752	-0.00993444757921	0.0905696968879	0.0907951374372	-0.0307054476231	-0.00216742570452	0.118795736909	0.00498138819103	0.190962096015	-17.3477742509	-5.08656929683	-10.3080627617
17	3.65941083244	3.0641267843	0.200347881384	6.62762446306	-3.33602541711	4.88176739006	0.382063348171	-0.501555419395	0.3007962057	0.577225736073	-0.373723075774	0.413919692239	-0.184392352185	-0.160591901792	-0.0145877364344	0.152831500046	-0.0369028428371	0.0581958933203	0.199071355849	-0.0406143603297	0.169006263013	-31.6465720799	-9.06935411268	-3.36567014584
18	1.9593587841	-0.564871240623	-0.507116907763	2.44277396482	0.372229890256	1.78259210361	-0.040664420419	0.195657013555	-0.272973429893	-0.0957766364132	-0.000198701710546	-0.0477599023775	0.346015271441	0.0949320658656	0.0750327783937	0.149202950765	0.0347997301065	0.00644618101696	0.137648955147	-0.0546220416512	0.153740012328	-46.4015005548	-25.4362419497	-55.9417602854
19	1.12877580849	-0.0101942535615	0.368857747717	1.10003272977	-0.113897799535	1.56572279256	0.0908833251677	0.00384394770864	-0.124704513337	-0.0183850223434	-0.0860493228243	-0.0472479534075	0.195227257859	0.107068845065	0.00765296272121	0.0989116707886	0.00297210990994	0.0194604735536	0.156360125871	-0.045848960819	0.178747079665	-35.574550629	-18.3753115526	-40.7314337254
20	0.478232345849	-0.123882883154	0.577058330582	1.96615154885	0.0430705714693	1.14726423536	0.0416733305804	0.138996701189	0.0080452872294	-0.186325435933	-0.0618464179308	-0.0536623846725	-0.0870989357714	0.0975041232786	0.0129188170581	0.0955642545204	0.00654413357203	0.0145883099837	0.100052606798	-0.0256531757227	0.112017639958	-46.0356881139	-9.57091369571	-53.130944986
21	0.4068799935	-0.00150585946858	0.0101062086866	0.868079417893	-0.227277166142	0.523368263631	0.276578518311	0.000287498029452	0.266780773985	0.182971706431	-0.126282335199	-0.237231079293	-0.653874958501	0.255376649261	0.197512525901	0.754957350078	-0.285151540529	0.227392393307	0.1666389616	0.0984798572416	0.169621373431	-19.1445447218	102.155586225	-58.7418214227
22	1.40864379996	0.263909107436	-0.491810080364	0.0620254135023	-0.00154929081762	1.00991106612	0.101706414832	-0.0075082631171	0.0747737556801	-0.266318326499	-0.0221463688751	-0.0750901563723	-0.106289803322	-0.0181410393176	-0.130358427543	0.67404926579	-0.016535447972	0.111913422634	0.167405538032	0.010619107705	0.173419040237	-30.798331057	104.29706279	-54.6527859886
23	1.93724038483	-0.261129123426	0.150443212089	1.04161931023	0.233124774657	0.0763361233266	0.0302587735255	0.139542028193	0.218503438031	-0.3843692914	-0.0796863869679	-0.411745386531	-0.33971870091	0.426575944374	0.105415191963	0.487465794155	-0.266563422973	0.153573429911	0.507593991822	0.00545655790954	0.326653734505	-19.5744602932	103.478971909	-33.0992067331
24	0.633732905763	0.178035829761	-0.417721799763	0.205727532352	-0.714137474545	2.56439533954	0.346304649162	0.0813914400175	0.428940172441	-0.105174636773	-0.0443746913291	0.28899918361	-0.479333573739	-0.10883882342	-0.272197487494	0.744199981257	0.0371653913779	0.126232782038	0.20506008453	0.0262120626483	0.335616416999	-40.5208514897	108.271401451	-51.9307923288
25	0.921866082701	0.240033486754	-0.787981117718	1.92489918583	-2.30383413068	3.38458801705	0.242883103544	-0.0761102324486	0.0618214205793	0.00590365276232	-0.180033972397	-0.0316060874804	-0.423963026484	0.0462946798586	-0.0787819070757	0.410496292698	-0.0273784517437	0.0451281953889	0.154213593428	-0.0156889210268	0.133168338023	-38.2167744592	97.6152624124	-46.133302752
26	1.89067619673	-0.666429974716	-0.206630081905	0.434143399433	0.33335900297	1.5573667035	0.066598209977	-0.14488682857	-0.0550121769804	-0.0258555090091	-0.0325062034482	0.045554182626	-0.18304925019	0.12210913957	-0.0310551667421	0.312402649224	-0.0747041460596	0.0255122726638	0.151011288263	0.0243990963821	0.163743891276	-30.3512288661	89.2426851502	-44.9931696925
27	0.897487304379	-0.0857521904507	0.349087547205	0.558444382056	-0.173092330871	0.171455269283	0.0596558477253	-0.109383663393	-0.124399683905	0.0983546050068	-0.0577948000963	-0.224687396628	-0.370598156188	0.362604877699	0.0337819612936	0.351496504349	-0.247821825612	0.035003421251	0.314944018061	0.0375260301035	0.230795284863	-15.0435450196	90.020675467	-50.4308967551
28	5.4636222798	4.08202007533	0.161360795196	3.13856930786	0.0431563066881	0.074139685856	-0.0733336994061	0.156891596281	-0.0926012913096	-0.334284631784	0.16946143731	-0.225702760842	-0.0487846620425	0.266690394011	0.00373169651738	0.338786772557	-0.108691173813	0.0696883016588	0.219276423435	0.0663158619283	0.225362346661	-17.1614802878	83.0352679208	-56.8131996668
29	5.1416133467	-4.3366607547	-0.273125501398	6.55578454498	-2.78809724067	3.61985760574	0.312119266807	0.316720478067	-0.137878630433	-0.493870927692	-0.241564201471	0.168592771242	-0.252954759959	0.0755399909941	-0.0516579446145	0.387383966337	-0.0262627457445	-0.0122533092935	0.132295232999	-0.0303407595336	0.134645043561	-30.8595488301	86.6394732342	-62.6414916203
30	2.42091009727	0.16467845805	0.588301947067	1.70907343493	0.329205036405	1.11942472411	0.00792936632908	-0.0889126789127	0.257652931703	-0.0955194779626	-0.0128701499642	-0.0569614328779	-0.369034606451	0.210043116155	0.0337530876871	0.263989370225	-0.107070628669	0.0295070101322	0.17918701199	-0.00713503891805	0.143798572319	-45.3499344095	103.321056357	-10.7825374895
31	1.51721850424	0.208751085302	-0.248374332449	1.09198122532	0.164193986156	1.19617408028	0.132880504452	-0.0467107013987	0.152974640138	-0.142560101504	-0.101578940121	-0.0796561802338	-0.364748516267	0.262429967525	-0.0104690706057	0.275948796939	-0.0939586742205	0.0356394698738	0.217606773821	0.00350192833889	0.13192639749	-34.8107510907	96.2006401242	-25.7112047615
32	2.34486907801	-0.577867240981	0.268674832534	1.87303011885	0.284084635306	1.45937173593	0.0114239292182	-0.131799375344	-0.0574051986833	0.0613564054439	-0.0555293293034	0.0468329970744	0.00513812455611	0.204280188123	0.0386051134443	0.153198848039	-0.058316439756	0.0164158246652	0.139487375179	0.019957463803	0.0956310534111	-46.1752452463	87.5001719044	-13.7526669569
33	2.18141996946	0.281162748733	0.768675437388	0.941366744661	0.611373439132	2.20387086164	0.0782016209577	0.0101301549463	-0.246205926657	0.011791013233	-0.0488311558145	0.023001094277	0.266472702148	0.00163740449113	-0.0312793817939	0.171495678104	0.00628746108519	0.0256795279549	0.0800543287696	0.000874974987339	0.177684689725	-59.0044389238	54.7273941842	-23.1310355204
34	1.72046439657	0.0338915789411	0.268188796673	0.847670863417	0.51106254261	2.14172343825	0.0111921562579	0.0817077965483	-0.1203245979	-0.0237390637849	-0.0586051582456	0.00941824150788	0.116611717837	0.139090323962	0.0391079026868	0.129644381722	0.000167951965927	0.0193515799167	0.104712857405	0.0187595976744	0.117437481623	-43.6390021217	61.0793825178	-33.4498938642
35	0.889154664264	0.384953247319	0.491707848488	0.904550031019	0.473505792119	1.94720053877	-0.0432277044158	-0.0095358231928	0.0647208570648	0.0126448963757	-0.0399923281584	0.179420262656	-0.068090977391	0.0128853845027	0.102757298216	0.10490869709	0.00837740757335	0.0206778973718	0.0701196825064	0.00477041856193	0.148184036538	-55.6108513356	70.4006827596	-23.0348104155
36	1.05003288859	-1.17278897316	0.731137645678	2.25703360962	0.640075006766	3.37608446044	0.0559194036257	-0.0507685538475	-0.085422990784	-0.113389815995	-0.0438923454213	-0.207365268729	0.140713395398	0.323243861743	-0.0222607725433	0.162131892671	-0.0248582603713	0.0417016450066	0.235131946918	0.0892704975833	0.201139176149	-11.3044025943	53.996533486	-49.2294128126
37	1.36487284924	-0.92722331168	0.796159844513	9.0468052155	-0.5737827216	3.58790184815	0.0370290077811	-0.0929941580907	-0.0687601222578	0.0856183208875	-0.274500988273	-0.286717495671	0.252646495007	0.185358281137	0.228072015096	0.220572544518	0.0162006129355	0.00692431189057	0.27699078382	0.11725003346	0.301885014669	-7.04912001448	44.7820259651	-37.0232814973
38	3.0650397329	-1.24727638986	0.742821567686	2.02882592617	-0.868793726193	1.18180729853	0.0372620708853	0.525992516894	-0.220527461253	-0.131545016183	-0.13864281262	0.118519793614	0.250654192559	0.0553991782232	0.120904381801	0.22097248885	-0.00895197165985	0.0176680034434	0.318664608761	-0.00971418380221	0.132047063482	-32.8256234922	55.4099781235	-46.841715298
39	2.92549943081	-0.191592449752	-0.329581238223	1.2804222907	-0.134577722491	0.575997523941	0.25832346066	0.128029793727	-0.394710401967	-0.033621928121	-0.154484853418	0.0296449153536	0.188197436721	-0.0288713649237	-0.100386180721	0.253572529215	0.0287053341638	-0.0160617570252	0.187049455703	-0.00416021403775	0.185583519356	-25.5215004491	48.942981821	-34.4711036414
40	3.87638099389	-1.47809580238	-0.368670775012	2.00604237142	-0.560668308786	1.42455062414	-0.00360583876869	-0.0713380922045	-0.0481076693935	0.192239871166	-0.0750838115541	-0.0560573245652	0.000252941113948	0.204378801491	0.0860565065593	0.180552748362	-0.0245998339798	-0.0191613954867	0.175921966672	0.0390697178594	0.125476127792	-23.6002007935	59.0128389791	-29.7844819782
41	1.75927626807	-0.00614106228518	-0.111918745056	1.92612060187	-0.572486159878	2.45890905211	0.0232582187008	-0.0632837661171	0.0779820543869	0.0843122850312	-0.061002476164	-0.0767610607369	-0.163229167791	0.144617521374	0.0401675738282	0.133840844053	-0.0358999717618	0.00437825813517	0.151818880894	0.0299958479845	0.12415643132	-24.3037603317	66.9891566975	-38.1463437284
42	1.46703314627	0.446032680738	0.33380479343	1.72564663042	0.681453352814	1.50181530291	-0.0407367930865	0.0697647685543	-0.0128642509891	-0.158500824913	-0.0436933142361	-0.192650619345	-0.150224816022	0.129045656549	0.0946806676055	0.177291930365	-0.0243239748497	0.00818270744276	0.191965706895	0.0570025124817	0.15582185451	-18.6053387111	65.3597105673	-53.0545801135
43	0.373297830315	-1.5553530741	-1.27709726397	6.62931702546	5.44361849619	4.46489814672	0.0555152646227	0.0964203547098	0.111147329801	-0.26835396017	0.169509903181	-0.624653782889	-0.294868805259	0.297420214409	-0.245462185919	0.225753053357	-0.0806711667725	0.00155568034169	0.301722730483	0.0840478664178	0.25691582002	-11.5776872643	71.6772495359	-51.37157136
44	2.12712069013	-0.435501054379	-0.446818114361	3.97013792404	-0.895749097754	0.343393284521	-0.0506349759344	-0.0693875699917	0.167071126118	0.428136007457	-0.264559172167	-0.910133309727	-0.183546145386	0.385410919473	0.330192500768	0.249177461735	-0.122175172098	-0.074719996009	0.354638722229	0.0650866958644	0.302456855217	-6.47870985608	68.959060386	-37.2656415759

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 130 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 131 through 197 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 198 through 312 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 23 through 80 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 81 through 130 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 131 through 150 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 151 through 175 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 176 through 239 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 240 through 281 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 282 through 295 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 296 through 312 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 23 through 61 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 62 through 130 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 131 through 175 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 176 through 281 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 282 through 296 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 297 through 312 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 23 through 130 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 131 through 261 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 262 through 312 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 23 through 123 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 124 through 140 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 141 through 161 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 162 through 175 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 176 through 197 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 198 through 261 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 262 through 281 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 282 through 295 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 296 through 312 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 23 through 130 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 131 through 261 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 262 through 312 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 23 through 130 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 131 through 261 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 262 through 312 )
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 23 through 115 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 116 through 130 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 131 through 150 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 151 through 175 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 176 through 197 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 198 through 261 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 262 through 281 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 282 through 295 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 296 through 312 )

-
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