PDB-4tza: TGP, an extremely thermostable green fluorescent protein created ...

ID or keywords:

Entry

Database: PDB / ID: 4tza

Title

TGP, an extremely thermostable green fluorescent protein created by structure-guided surface engineering

Components

Fluorescent Protein

Keywords

FLUORESCENT PROTEIN / thermostable / engineered

Function / homology

Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Close, D.W. / Bradbury, A.R.M.

Citation

Journal: Proteins / Year: 2015
Title: Thermal green protein, an extremely stable, nonaggregating fluorescent protein created by structure-guided surface engineering.
Authors: Close, D.W. / Paul, C.D. / Langan, P.S. / Wilce, M.C. / Traore, D.A. / Halfmann, R. / Rocha, R.C. / Waldo, G.S. / Payne, R.J. / Rucker, J.B. / Prescott, M. / Bradbury, A.R.

History

Deposition	Jul 9, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 29, 2014	Group: Database references
Revision 1.2	Feb 4, 2015	Group: Derived calculations
Revision 1.3	Jun 3, 2015	Group: Database references
Revision 1.4	Feb 17, 2016	Group: Data collection / Database references
Revision 2.0	Nov 15, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4tza.cif.gz	630.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4tza.ent.gz	433.8 KB	Display	PDB format
PDBx/mmJSON format	4tza.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tz/4tza ftp://data.pdbj.org/pub/pdb/validation_reports/tz/4tza	HTTPS FTP

-
Related structure data

Related structure data	4tzgC C: citing same article (ref.)
Similar structure data	4ppl-2 2z6z-6 6myb-5 2otb-1 3nez-2 5hzt-3 5h89-2 5hzu-9 5lk4-d 2gx2-8 4ppk-2 5h88-3 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 - HomologyF&H Search

Related structure data

4tzgC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

C: Fluorescent Protein

A: Fluorescent Protein

B: Fluorescent Protein

D: Fluorescent Protein

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

1

C: Fluorescent Protein

defined by author&software
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Fluorescent Protein

defined by author&software
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Fluorescent Protein

defined by author&software
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Fluorescent Protein

defined by author&software
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.1999, 141.22, 69.0897
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Fluorescent Protein Mass: 28252.732 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pETCK3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	CRQ is the chromophore that folds from the amino acids QYG, which are encoded in the original ...CRQ is the chromophore that folds from the amino acids QYG, which are encoded in the original sequence. MGAHA represents N-terminal residues added when expressed from the plasmid. SGGGSGGGASGKPIPNPLLGLDSTHHHHHH are C-terminal SV5 and His Tags.

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG MME 2000, 0.1 M Tris-HCl pH 7.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.542 Å / Relative weight: 1
Reflection	Resolution: 1.9→28.6 Å / Num. obs: 72746 / % possible obs: 99.2 % / Redundancy: 4.9 % / B_iso Wilson estimate: 23.7964299494 Å² / R_merge(I) obs: 0.062 / Net I/σ(I): 12.3

-
Processing

Software

Name	Version	Classification
HKL-3000	1.9_1685	data collection
iMOSFLM		data reduction
SCALA		data scaling
Coot		model building
PHENIX	(phenix.refine: 1.9_1685)	phasing
PHENIX	(phenix.refine: 1.9_1685)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→28.5861694308 Å / SU ML: 0.187768078998 / Cross valid method: FREE R-VALUE / σ(F): 1.33087988092 / Phase error: 21.7324419422

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.200305594674	2047	2.84887200256 %	Random
R_work	0.173763175365	69806	-	-
obs	0.174538516473	71853	98.0112125056 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 35.4435785015 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→28.5861694308 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7010	0	0	816	7826

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00688551734927	7209
X-RAY DIFFRACTION	f_angle_d	1.23434342435	9720
X-RAY DIFFRACTION	f_chiral_restr	0.0408730419139	982
X-RAY DIFFRACTION	f_plane_restr	0.0050412106213	1264
X-RAY DIFFRACTION	f_dihedral_angle_d	14.3346904396	2746

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 (%)
1.9-1.9442	0.435782929563	112	0.43276706847	3969	X-RAY DIFFRACTION	84.8088113051
1.9442-1.9928	0.249948203001	144	0.231515157764	4679	X-RAY DIFFRACTION	99.6281759967
1.9928-2.0467	0.210330296748	136	0.186941801159	4699	X-RAY DIFFRACTION	99.8966942149
2.0467-2.1069	0.21795455035	137	0.182959517019	4669	X-RAY DIFFRACTION	99.9168399168
2.1069-2.1749	0.2036556934	155	0.185503493934	4664	X-RAY DIFFRACTION	99.7929177884
2.1749-2.2526	0.336616676393	111	0.296793276224	4453	X-RAY DIFFRACTION	94.1224994844
2.2526-2.3427	0.306904897691	121	0.235478252235	4419	X-RAY DIFFRACTION	94.0542780195
2.3427-2.4493	0.231938170892	133	0.178271230811	4727	X-RAY DIFFRACTION	99.774173681
2.4493-2.5783	0.186227574878	160	0.174919422928	4699	X-RAY DIFFRACTION	99.7331691297
2.5783-2.7398	0.207855054492	142	0.166519828719	4717	X-RAY DIFFRACTION	99.7741273101
2.7398-2.9511	0.214383017688	147	0.174737497438	4738	X-RAY DIFFRACTION	99.7753267974
2.9511-3.2477	0.202928306442	128	0.169535042955	4763	X-RAY DIFFRACTION	99.8774760057
3.2477-3.7168	0.16676496596	140	0.157925605761	4771	X-RAY DIFFRACTION	99.6146044625
3.7168-4.6794	0.15983500125	139	0.125334013088	4835	X-RAY DIFFRACTION	99.6593868964
4.6794-28.5894	0.146896578699	142	0.1353675471	5004	X-RAY DIFFRACTION	99.4204018547

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	0.167617919963	-0.108295878956	0.0561535241033	0.0819901439007	-0.176289183464	0.189593876777	-0.0376146959854	-0.0716765742172	-0.0523358649365	-0.0448202466112	-0.125972330745	0.201500960784	-0.0179874695189	-0.207791781508	-0.00354238096881	0.10706187719	-0.00205462950408	0.00445440989744	0.17912419594	-0.0532015618484	0.160365935038	-7.17544736681	-8.52417454687	-27.2268026453
2	0.165872214962	0.0783955509243	0.0528688277599	0.0406720415275	-0.0803240142631	0.107542129157	0.0338632509112	0.0803330345352	-0.0255953212838	-0.0322469296928	-0.0495157759598	0.0615015266998	-0.0118916083666	-0.094474264951	-4.6931825371E-6	0.14810461295	0.0155459615242	-0.0190795477251	0.189521735083	-0.0437832874149	0.144880611363	-5.59442918668	-2.51796025344	-30.1416579336
3	0.205235068103	0.0251856261153	0.0381344548228	0.0294169790651	0.0247157771841	0.0146556263628	0.0123943448051	0.190533052954	-0.313336269195	0.0878404316259	-0.0783438477258	0.150845222477	-0.0209889435913	0.00734638896835	-0.056041287298	0.203883134411	0.0236904198139	0.0143887329654	0.204001393904	-0.0956801258783	0.192335251048	4.72088077424	-18.1262543011	-38.344902971
4	0.0337294505963	0.0254807793472	0.0248971195895	0.0349213118825	0.0384310692891	0.0877170203474	0.0133268682795	0.0499134197609	-0.0827749563117	0.163151770217	-0.010274648477	-0.296225008009	-0.0355428916017	0.0799786801036	-2.25127457777E-5	0.131497095968	-0.0139227666206	-0.0227955791281	0.109235503282	0.0131444388932	0.12836415943	7.92615896458	-0.140909879822	-26.4340100705
5	0.0408536054512	-0.0729097695191	0.0282427096445	0.0533467483153	-0.0705925699555	0.111423650573	-0.0342911147733	-0.17595654461	-0.125066495961	0.0241036302764	-0.077522413177	0.110724535783	-0.0299969059184	-0.0718689332491	-0.000520195572102	0.135677832037	-0.00937812331041	0.00336710818406	0.123812395421	0.00190463772674	0.175655902532	-1.30378935112	-9.77813162628	-24.3735522668
6	0.133630028862	0.175758674905	-0.125116487129	0.121274869819	0.078191657748	0.024304985875	-0.00226803166428	0.11677295774	0.0862059592658	-0.0208353429669	-0.0876065343196	-0.0707288890962	-0.115933892678	0.109378586879	-0.000730154123143	0.250917263705	0.0340478533517	-0.0114649483761	0.177968676665	-0.00183682172317	0.150142609262	5.53487667128	4.71153395025	-31.0677328819
7	0.0658827422237	0.0193340184593	0.0762953072994	0.10238073409	0.0496905899736	0.0449011454403	0.0726855139815	0.17484452214	-0.0188947743636	0.0185788570929	-0.173874584499	-0.0648485056945	-0.0895253323806	0.181301037738	0.00378639703382	0.17604628892	0.0156189209404	0.0127056441281	0.158488971715	0.0272464533501	0.0978022198106	8.23203359547	1.67001295099	-32.9048039231
8	0.254367355061	0.194549832873	0.115369446282	0.214058459505	0.0615966697885	0.151578019325	-0.103280819047	0.139050070721	-0.171444091638	-0.110829693637	0.0458054361659	-0.0229468193205	-0.0379296918152	-0.122200954645	0.0026733108784	0.238967107143	0.0504497950123	0.0120477638833	0.247198365929	-0.0267073288238	0.197190298636	4.38449484519	-9.41445156697	-37.5643991466
9	0.053739314279	-0.0820843554457	0.0742810177806	-0.0176082780238	-0.0887500763836	0.222063435009	-0.130345684774	-0.0663025782796	-0.00605121808961	-0.267051126394	0.0199910522848	0.0845239217938	-0.0827677523592	-0.0208610030335	-0.0397442752396	0.185383864611	0.0766172233107	-0.0391109691987	0.277927426966	-0.0436333382706	0.180758576524	-5.52699784577	-1.323709417	-36.4409398939
10	0.21289604452	-0.217340055674	0.205065292262	0.1720710609	-0.199015227175	0.144519598076	0.00841696795784	-0.195690814724	-0.0599798312228	0.00317754996488	-0.000318091196948	0.172173328922	0.11750489679	-0.102278689401	0.0339716261605	0.195378079711	-0.00868233470774	-0.0133296198947	0.208097656351	-0.0105396985356	0.152408819816	6.63560865715	0.402522401009	0.99918528118
11	0.236081306683	-0.125085152362	0.142733439141	0.078675441909	-0.134564101703	0.267950899785	-0.0138297550004	-0.177346108992	0.0245162187082	-0.0283823488298	-0.0181258142311	0.0169914253054	0.0174529164596	-0.102534366347	-0.00630486106953	0.195496514823	0.0238924067589	-0.0271344618764	0.171077230102	-0.0264842420051	0.129989890734	13.7071806559	4.27889765805	-0.0792153769332
12	0.244565865426	-0.291484013392	0.406259460457	0.171150740122	-0.235957146761	0.466171396224	0.0503541682873	0.0811395866363	0.505273360166	-0.112746599517	0.105338490244	0.790001259461	0.0682970741275	-0.126624016306	0.115314566215	0.149731493128	0.0402837311834	-0.135504235429	0.131800353494	-0.121152104537	-0.25024502812	10.075166715	3.42001460971	-8.40907893507
13	0.0692470248746	0.0828625245093	-0.0179616303434	0.0618422889335	0.0558791237481	0.185054868679	0.00325928593649	0.114605592454	0.136272676936	-0.0592979702634	-0.0821467460541	0.0639964733971	0.0961886116242	0.155399518104	0.000626404941413	0.200125551774	0.0279125141925	-0.0311463892803	0.165868884	0.0218862853445	0.193336206369	20.2821847394	9.67700520325	-10.1890496172
14	0.157701331315	0.133751582624	0.0555188905401	0.101017365626	-0.0107177518786	0.094582139609	-0.127783301535	0.0660324838463	-0.00796444707617	-0.07678831805	-0.049039035575	0.0460149321154	0.0396924440595	0.107907513677	-0.0156889661352	0.21351657584	0.0690344606601	0.00501859080472	0.222046157617	0.0285844987515	0.167159482581	19.7635858767	4.98567765299	-12.272921785
15	0.0714686419088	-0.0325645639874	-0.0364518552024	0.0603849394861	0.0491556350968	0.194019093589	-0.0287818510255	-0.109695272168	0.212388316124	0.0816198812328	0.0595366372781	-0.0637353155914	0.0397707308826	-0.00237428577649	0.00158913882103	0.144893266171	0.0337160925172	-0.0338877244352	0.113068162173	-0.0076845937056	0.199940078307	15.3367094966	12.8656683025	-2.25518255236
16	0.333914817703	-0.12517021558	-0.0373074930796	0.0544264492037	0.0104821519969	0.0403258331468	-0.0371296676123	-0.143734447962	0.0143244959282	-0.0779843928669	0.112877325435	-0.00702401735285	0.0806705239864	0.0486494149372	0.0413750381923	0.219990163103	0.0103163267182	-0.0420978338181	0.178485856205	0.0259921512877	0.135226216559	18.5149904265	0.725868020534	1.6315204823
17	0.237386012517	0.0875064312735	0.0835787950787	0.132484241877	-0.0396893333038	0.122290130115	-0.109572367125	-0.0548240719016	-0.0850123887401	-0.285887643757	-0.151636257338	0.0307718967341	0.0947609847819	0.0923190332856	-0.094837098762	0.365806413267	0.0420089838095	0.049382480718	0.108408150749	0.0564508694256	0.169158528865	18.0244642231	-42.6065880909	-19.3617204366
18	0.0535986997052	-0.00358700528501	0.0250876164762	-0.00441049530191	0.00918692329008	0.0225794397577	-0.0195332369665	0.00962206129399	-0.0315698695686	-0.107392260249	0.0114386268651	0.0553653616297	0.0175196400601	-0.0228410028945	-1.68558992643E-5	0.274577962103	0.00589211788578	-0.0029730362729	0.161486008834	0.03766569158	0.244700936696	11.7004666521	-44.4358632506	-15.2081597998
19	0.178801757148	0.0107261795976	0.196358613473	0.503218722765	-0.41502083395	0.528859670548	-0.0886856026834	-0.092881770648	-0.106728365448	-0.215366678345	-0.159911755353	-0.0639440826836	0.154131841863	0.173253881242	-0.583928734853	0.221305521568	0.0249153456575	0.0319655323984	0.145828666233	0.0829522473854	0.233677611754	19.8934021487	-36.2823921691	-13.8553141261
20	0.589594616318	0.0759383793882	0.33076831584	0.186241003476	0.0097914428014	0.180293921229	-0.0662281083483	-0.532543672734	0.0145586543378	-0.226116332519	-0.248543685272	-0.188752434	0.186309358702	-0.0397277380229	-0.0988360334572	0.319906826042	0.0827663826574	0.127262774666	-0.0771516753942	0.149745743089	0.257043344247	21.1246268731	-44.5467114724	-14.0237044801
21	0.0144655381675	0.0201151529939	-0.00402605709507	0.0165448071731	0.00314838882061	0.0202257114139	0.0424390897325	-0.122931725045	0.127426169024	-0.0882743557122	-0.0356596573164	0.0475828420701	0.139188275916	-0.041239105515	-3.15273630713E-6	0.178820029543	0.00638522252664	0.0562402278673	0.265834649121	0.0414110241141	0.244151585381	6.61076262879	-38.1016567789	4.76003274723
22	0.237059916077	0.105194216902	-0.0149763274057	0.275047621948	0.0994098484203	0.359897296741	-0.115745186833	-0.135986316502	0.0142965937953	0.0212139702639	-0.0885635113228	-0.0715781516312	-0.144301664182	0.135434633403	-0.0960722560856	0.224724234482	0.000476777593565	0.018005686731	0.212480107319	0.103550653521	0.351646535467	22.5769244261	-29.0755041361	-5.90427078494
23	0.0242252630916	0.078821531133	-0.0274514277158	0.185981938318	-0.176180952553	0.0849855050553	0.0293825577263	-0.13350985337	0.0810647983415	0.106198307677	-0.183490516846	-0.119358895494	-0.0478050400116	0.0164596349409	1.68154350765E-5	0.272082091988	0.0219517343914	0.0156342014979	0.261716659091	0.0120936840133	0.271376790435	19.2444559321	-31.7658873603	-2.76442872503
24	0.00728826707924	0.0112713812792	-0.044050841679	0.119110213924	-0.0372166522597	0.0254738903485	0.0436963720053	-0.00682089985913	-0.083976470651	-0.232728725944	-0.0350261055857	-0.029476410063	-0.10857623899	0.0737868992967	1.21645018194E-5	0.232895400252	0.0087413712451	0.0339945064777	0.232993763003	0.0782205759512	0.382478778662	24.5544827397	-30.9027818293	-15.3580674155
25	0.0822485262036	-0.173392344718	0.0494618721231	0.117448558436	-0.08993011979	0.0292814161949	-0.0101031284619	0.0793146805129	0.0438191266414	-0.0716337751885	0.0176972918607	0.0327660622657	-0.00204844662055	-0.0888546162373	-9.30506783191E-6	0.247272058257	-0.00595585978167	-0.0220037595165	0.168694680644	0.0705168199372	0.279104702007	11.6112091382	-32.4505230787	-15.330303545
26	0.325541800898	0.0634610496412	0.134296437657	0.22108130403	0.0335427946038	0.481163175703	0.112534053609	-0.0587644740638	0.0666384745433	-0.067456273104	0.0771924749737	-0.132938877775	-0.145511369954	-0.0867804452826	0.213934326179	0.177178198367	0.0815490801506	0.079692181159	0.248961987052	0.0853823594968	0.244390746516	-25.0770875218	-7.24656916636	-7.3288547271
27	0.267377573563	-0.0473906504801	-0.248464640776	0.49506341271	0.160257547994	0.411478871763	0.140300370617	-0.0114357897338	-0.136240487522	-0.152863644218	-0.00257251248653	-0.236376793328	-0.110759794461	-0.195987782857	0.0624476227073	0.156323069889	0.0604271082255	0.0675978839129	0.23608166006	0.072469781497	0.218698134881	-24.9756172778	-14.0851964288	-13.289293844
28	0.690920291204	0.162009025762	0.0988798596724	0.286007399855	0.2422479346	0.220202527551	0.296136583016	0.0471389328381	-0.219296968963	0.256678119238	-0.186053303579	-0.230012588089	-0.201814047932	-0.242119774477	0.105559070083	0.120034307412	0.108854632758	0.0731413369503	0.291880705436	0.0780180699196	0.226433032085	-24.0152666748	-15.8308468813	-5.04991622355
29	0.0510839069442	-0.0803880821146	-0.031735947778	0.289779587021	-0.0990163833309	0.150085792052	0.204443210036	-0.297126944429	-0.129535517718	-0.557548966843	-0.154715663719	-0.397607119806	0.0476691577706	-0.361814574547	-0.00446644762712	0.210591676971	0.00433250676726	0.0382240263983	0.344020524391	0.0287624399756	0.381931165759	-21.0706210454	-23.4503285737	-16.7794754793
30	0.00671492783893	0.017498275995	-0.00639253939923	0.0706860710864	-0.0189975313628	0.132828318697	-0.0310551532075	0.0420008750051	0.0221153767057	-0.115062602297	0.0781820325449	-0.251174944029	0.0490160155421	-0.144405926232	-1.40772415939E-6	0.231681554918	0.0451224568599	0.0764532924291	0.273818116591	0.0352262571478	0.428714682106	-19.5182889732	-24.7107138962	-13.4012821561
31	0.0267018990704	0.000850938126466	-0.0501303650876	0.133058556783	-0.182913634937	0.155176306651	0.0703863221833	-0.0398285241372	0.0474733584586	-0.332078300243	-0.0798334999912	-0.201441194308	-0.191023936088	-0.255994976266	0.00111516414102	0.216213578752	0.0585464927447	0.0614074206324	0.336369954624	-0.00996935584008	0.307726843429	-27.188182245	-15.7689105262	-20.2154221016
32	0.105770516116	0.0766904619518	-0.0811345067368	0.104996618222	-0.0494209661737	0.112656701007	0.0971883899116	-0.102959709054	0.0736619919748	-0.269126513757	-0.252034561585	-0.24738385979	-0.00103394587264	-0.0965148878666	0.00980428311491	0.168301868965	-0.0241808280754	0.12489572338	0.266371907299	0.00588278359536	0.417055399224	-16.6214064385	-10.5206561098	-14.8813640035

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resseq 2:32)
2	X-RAY DIFFRACTION	2	chain 'C' and (resseq 33:66)
3	X-RAY DIFFRACTION	3	chain 'C' and (resseq 67:86)
4	X-RAY DIFFRACTION	4	chain 'C' and (resseq 87:99)
5	X-RAY DIFFRACTION	5	chain 'C' and (resseq 100:123)
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 124:151)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 152:179)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 180:200)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 201:217)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 2:32)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 33:77)
12	X-RAY DIFFRACTION	12	chain 'A' and (resseq 78:135)
13	X-RAY DIFFRACTION	13	chain 'A' and (resseq 136:163)
14	X-RAY DIFFRACTION	14	chain 'A' and (resseq 164:179)
15	X-RAY DIFFRACTION	15	chain 'A' and (resseq 180:200)
16	X-RAY DIFFRACTION	16	chain 'A' and (resseq 201:217)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 2:20)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 21:32)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 33:99)
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 100:123)
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 124:135)
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 136:163)
23	X-RAY DIFFRACTION	23	chain 'B' and (resseq 164:179)
24	X-RAY DIFFRACTION	24	chain 'B' and (resseq 180:200)
25	X-RAY DIFFRACTION	25	chain 'B' and (resseq 201:217)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 2:32)
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 33:99)
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 100:133)
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 134:163)
30	X-RAY DIFFRACTION	30	chain 'D' and (resseq 164:179)
31	X-RAY DIFFRACTION	31	chain 'D' and (resseq 180:200)
32	X-RAY DIFFRACTION	32	chain 'D' and (resseq 201:217)

-
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