PDB-4lln: Crystal structure of S. aureus MepR-DNA complex

ID or keywords:

Entry

Database: PDB / ID: 4lln

Title

Crystal structure of S. aureus MepR-DNA complex

Components

MepR
Palindromized mepR operator sequence

Keywords

TRANSCRIPTION/DNA / multidrug resistance / winged helix-turn-helix / transcription repression / mepR operator / TRANSCRIPTION-DNA complex

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.842 Å

Authors

Birukou, I. / Brennan, R.G.

Citation

Journal: Nucleic Acids Res. / Year: 2014
Title: Structural mechanism of transcription regulation of the Staphylococcus aureus multidrug efflux operon mepRA by the MarR family repressor MepR.
Authors: Birukou, I. / Seo, S.M. / Schindler, B.D. / Kaatz, G.W. / Brennan, R.G.

History

Deposition	Jul 9, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 20, 2023	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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4lln.cif.gz	480.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4lln.ent.gz	393.5 KB	Display	PDB format
PDBx/mmJSON format	4lln.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	4lllC 1z9cS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4lll-1 4lll-3 4lll-2 3q5f-d 5hlg-3 5hlh-4 6za0-d 5hlg-4 4cj0-d 2emt-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4lllC

1z9cS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: MepR

B: MepR

G: Palindromized mepR operator sequence

H: Palindromized mepR operator sequence

C: MepR

D: MepR

E: Palindromized mepR operator sequence

F: Palindromized mepR operator sequence

I: MepR

J: MepR

K: Palindromized mepR operator sequence

L: Palindromized mepR operator sequence

142 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MepR

B: MepR

G: Palindromized mepR operator sequence

H: Palindromized mepR operator sequence

defined by author&software
47.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: MepR

D: MepR

E: Palindromized mepR operator sequence

F: Palindromized mepR operator sequence

defined by author&software
47.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: MepR

J: MepR

K: Palindromized mepR operator sequence

L: Palindromized mepR operator sequence

defined by author&software
47.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.343, 76.231, 109.410
Angle α, β, γ (deg.)	90.61, 104.75, 106.27
Int Tables number	1
Space group name H-M	P1

#1: Protein	MepR Mass: 16262.288 Da / Num. of mol.: 6 / Fragment: MepR Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mepR / Production host: Escherichia coli (E. coli) / References: UniProt: Q5Y812
#2: DNA chain	Palindromized mepR operator sequence Mass: 7365.814 Da / Num. of mol.: 6 / Fragment: palindromized mepR operator / Source method: obtained synthetically Details: this is a palindromized version of mepR operator sequence naturally occurring in S. aureus

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.15 Å³/Da / Density % sol: 70.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.14M CaCl2, 0.7M Na Acetate, 14% 2-propanol, 30% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2012
Radiation	Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.84→50 Å / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / B_iso Wilson estimate: 70.91 Å² / R_merge(I) obs: 0.096 / Net I/σ(I): 31.73

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction
ADSC	Quantum	data collection
DENZO		data reduction
SCALEPACK		data scaling
HKL-3000		data scaling
PHENIX	(Phaser)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1z9c

1z9c

Resolution: 2.842→44.835 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.4 / σ(F): 1.97 / Phase error: 31.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2408	1997	4.18 %
R_work	0.2062	-	-
obs	0.2076	47765	88.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 116.8066 Å²

Refinement step

Cycle: LAST / Resolution: 2.842→44.835 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6345	2934	0	0	9279

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9723
X-RAY DIFFRACTION	f_angle_d	0.915	13760
X-RAY DIFFRACTION	f_dihedral_angle_d	25.261	3737
X-RAY DIFFRACTION	f_chiral_restr	0.044	1589
X-RAY DIFFRACTION	f_plane_restr	0.003	1268

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 (%)
2.8424-2.9134	0.5503	78	0.4162	1782	X-RAY DIFFRACTION	48
2.9134-2.9922	0.4145	110	0.3738	2525	X-RAY DIFFRACTION	69
2.9922-3.0802	0.3756	118	0.3034	2699	X-RAY DIFFRACTION	74
3.0802-3.1796	0.3009	130	0.2411	2964	X-RAY DIFFRACTION	81
3.1796-3.2932	0.2583	137	0.2151	3202	X-RAY DIFFRACTION	87
3.2932-3.425	0.2544	154	0.2166	3492	X-RAY DIFFRACTION	95
3.425-3.5808	0.2994	155	0.2245	3582	X-RAY DIFFRACTION	98
3.5808-3.7695	0.2885	159	0.217	3647	X-RAY DIFFRACTION	99
3.7695-4.0056	0.2482	159	0.2062	3655	X-RAY DIFFRACTION	99
4.0056-4.3146	0.2143	159	0.1758	3619	X-RAY DIFFRACTION	99
4.3146-4.7484	0.1877	160	0.1812	3656	X-RAY DIFFRACTION	99
4.7484-5.4345	0.2736	158	0.2021	3647	X-RAY DIFFRACTION	99
5.4345-6.8429	0.2515	161	0.2312	3670	X-RAY DIFFRACTION	100
6.8429-44.8403	0.1778	159	0.1713	3628	X-RAY DIFFRACTION	99

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	0.0712	0.0271	-0.0136	0.0085	-0.0068	0.0044	-0.071	0.022	-0.0218	0.0712	0.081	0.0178	-0.0841	-0.055	0.0341	0.3845	-0.093	-0.1194	0.4735	-0.0296	0.0345	-14.0485	57.0887	35.4798
2	0.3229	-0.1294	0.3364	0.228	-0.2901	0.4851	-0.0869	0.2085	0.1551	-0.0541	-0.129	-0.1096	0.0313	0.1983	-0.0195	0.2302	-0.0361	-0.1087	0.1586	-0.0032	0.2576	-7.3481	75.8938	34.3277
3	0.1381	-0.0641	-0.0591	0.2119	0.1515	0.1055	-0.1242	0.0616	0.0971	0.0351	0.2524	0.0616	-0.2185	0.1194	0.0088	0.4057	-0.0092	-0.04	0.302	0.0569	0.2405	-10.8231	82.9379	36.8241
4	0.0254	-0.0293	-0.0114	0.0304	0.0143	0.0173	-0.0027	-0.0875	-0.0397	0.0385	0.1393	0.003	-0.0802	-0.1079	0.0209	0.947	0.157	-0.2711	0.3088	-0.1083	0.6772	-3.4569	57.0227	43.1644
5	-0.0017	-0.0019	0.0032	0.0045	-0.0065	0.0023	-0.0118	0.0027	-0.0832	0.1483	0.2795	-0.1074	0.0203	0.1077	0.0751	0.5628	0.0955	-0.1705	0.5046	-0.2453	0.7095	1.9939	55.3164	27.7653
6	0.2931	-0.2198	0.0811	0.274	0.0074	0.1405	-0.3405	0.1547	0.0074	0.3263	0.1135	-0.1146	0.1316	0.0156	-0.0501	0.4529	-0.1209	-0.0307	0.3663	0.0102	0.2374	-10.414	61.7402	23.3875
7	-0.0032	0.0131	-0.0047	0.0842	0.0006	0.0019	-0.01	-0.0855	-0.1582	0.0282	0.0222	0.0442	0.0679	-0.0782	0.0866	0.1881	-0.287	0.2416	0.2619	0.0499	0.1158	-27.0034	49.8234	24.9607
8	0.1584	-0.0752	0.167	0.1086	-0.076	0.1715	0.0675	-0.184	-0.1343	0.0967	0.0959	0.1757	0.0733	-0.3067	0.0902	0.3002	-0.0708	0.141	0.4658	0.0553	0.259	-37.1745	53.0613	25.7236
9	0.0058	0.0598	0.0277	0.2889	0.0172	0.0374	0.1235	0.1752	0.0874	0.233	0.115	-0.2248	0.0303	-0.0629	0.1326	0.273	-0.028	0.0018	0.4614	-0.0855	0.3567	-14.4991	49.0835	21.1143
10	0.2119	0.0612	0.1809	0.0973	0.1359	0.241	-0.1646	-0.0096	-0.0427	-0.0972	0.0193	0.0727	-0.0338	0.1033	-0.0358	0.6537	-0.268	0.0276	0.4045	0.0646	0.2176	-9.8744	88.7312	12.3398
11	0.2566	0.1876	-0.0446	0.1667	-0.0556	0.0345	0.0231	-0.1163	0.3363	-0.0602	0.0145	0.2116	-0.1727	-0.0947	-0.024	0.3139	-0.1903	0.0637	0.2439	0.1156	0.4999	-24.4629	75.2117	24.6689
12	0.2241	0.0203	-0.0906	0.0113	0.0194	0.0561	0.0516	-0.2895	0.0788	0.032	0.1429	0.1311	0.1188	-0.014	0.197	0.1393	-0.5869	0.6258	0.647	-0.0793	0.4567	-39.3328	56.1541	41.5207
13	0.1468	0.0341	0.0922	0.1076	-0.0097	0.0786	0.0475	-0.1216	0.3573	-0.033	-0.117	0.0415	0.117	-0.0788	-0.0743	0.403	-0.2269	0.1464	0.5694	0.0356	0.5515	-38.7913	55.9812	40.9171
14	0.1477	0.0414	0.0625	0.2102	0.1837	0.1656	-0.2114	0.0389	0.262	-0.4601	-0.083	0.3857	-0.136	-0.0477	-0.59	0.6321	-0.4805	-0.094	0.0823	0.0591	0.365	-21.8913	75.0023	24.3021
15	0.0017	-0.0027	0.0003	0.0068	0.0104	0.015	-0.0544	0.0173	0.055	-0.0882	-0.0383	0.1049	0.0802	0.4284	0.0001	0.7375	-0.1702	-0.0462	0.5665	0.0938	0.8203	-12.5433	93.8173	17.7294
16	0.036	0.0109	-0.041	0.0174	-0.0122	0.0509	0.0164	-0.0227	-0.0482	-0.035	0.0017	0.2957	-0.0384	0.0179	-0.0254	0.4797	-0.0178	-0.1899	0.2366	0.0408	0.523	-58.4418	44.7014	5.8119
17	0.284	0.1966	0.0375	0.1467	0.0275	0.0201	0.3022	0.1447	-0.2367	-0.2	-0.0866	-0.2035	-0.1612	-0.0107	0.1584	0.3728	-0.0105	-0.0437	0.1663	0.0438	0.2159	-41.212	32.5744	10.6852
18	0.0609	0.0048	0.0627	0.0533	0.0653	0.0691	0.219	0.0246	-0.0305	0.1415	-0.2254	0.1952	0.147	0.0187	0.0318	0.3807	0.0588	0.052	0.3769	0.1441	0.5749	-46.2507	34.3984	17.3436
19	0.0058	0.0097	0.005	0.0052	0.0031	0.0076	-0.0279	-0.119	0.058	0.0364	-0.0125	0.0582	0.019	-0.1143	0	0.6746	-0.1307	-0.0223	0.728	0.0301	0.9523	-68.5642	31.1316	8.7293
20	0.0276	0.078	0.0398	0.0853	0.0481	0.0421	0.1687	0.0117	-0.1735	0.0969	-0.0038	-0.0222	0.3056	-0.1131	0.1808	0.35	-0.0458	-0.1821	0.435	-0.004	0.4107	-58.7184	38.772	-5.4296
21	0.0966	-0.053	0.0019	0.0681	-0.0048	0.0044	0.0108	0.011	0.0151	0.0202	0.1446	0.084	-0.0783	-0.025	0.1266	0.1836	0.1329	0.0484	0.4026	-0.0834	0.1306	-54.789	54.0427	-9.2203
22	-0.0013	-0.0007	-0.0017	0.0035	-0.0003	-0.0021	0.1037	0.052	-0.0376	-0.0133	0.1553	0.013	-0.056	-0.029	-0.0001	0.9548	0.0801	-0.0623	0.6882	0.1286	0.6853	-57.6502	59.2735	-19.0953
23	0.0209	0.0304	0.032	0.0367	0.0201	0.037	-0.0053	0.1354	0.1579	-0.2431	0.0814	0.4175	-0.0441	-0.1346	0.0338	0.432	-0.0903	-0.24	0.4494	0.0542	0.6338	-68.3162	38.1221	-5.6261
24	0.101	-0.0066	-0.0625	0.0147	-0.019	0.0817	0.0082	0.165	-0.1291	-0.0723	-0.1094	-0.0118	0.16	0.0088	-0.0709	1.0954	0.3116	0.1367	0.3744	-0.3072	1.0525	-33.8649	19.251	-4.0629
25	0.0424	0.0563	-0.0103	0.0747	-0.0712	0.1251	0.0607	-0.1316	-0.1481	0.0841	-0.4289	-0.3719	-0.3991	0.2661	-0.2831	0.6119	0.0703	-0.0359	0.359	-0.0308	0.668	-41.9791	48.5334	-3.4447
26	0.0147	0.0215	0.0289	0.0319	0.0429	0.0612	-0.0942	0.0149	0.0417	-0.0101	-0.1278	0.0304	-0.1429	-0.0583	-0.0848	1.4416	0.3408	-0.2457	0.3385	0.036	0.8515	-47.6026	73.6014	-9.6033
27	0.0145	-0.0101	-0.0109	0.009	0.0077	0.0076	-0.2189	0.042	-0.0915	0.0324	-0.1062	0.0006	0.0453	-0.0942	-0.0048	1.0992	0.1731	0.2713	0.442	-0.1292	1.4146	-51.2687	73.8154	-2.3605
28	0.4609	-0.0488	0.1851	0.1696	-0.092	0.11	0.1237	0.2934	0.0874	-0.2684	-0.2923	-0.1925	-0.06	0.1648	-0.3638	0.508	0.3738	-0.2492	-0.0226	-0.1512	0.5714	-42.5557	47.0413	-4.0986
29	0.0557	-0.0026	-0.0443	0.0032	0.0101	0.3085	-0.01	0.185	-0.0258	0.1262	-0.1926	-0.0023	0.1102	0.0219	-0.112	1.1251	0.5711	-0.1403	0.4348	-0.0167	1.1511	-29.1926	20.8642	-4.8439
30	0.0157	-0.0533	0.0756	0.111	-0.1553	0.2402	0.1223	0.0242	0.0476	-0.0665	-0.09	-0.0281	0.0599	0.1445	-0.012	0.1984	-0.0879	0.0731	0.4814	-0.1974	0.1925	-11.338	108.1259	52.7912
31	0.0122	-0.0001	0.0057	0.0696	-0.0022	0.0304	-0.1703	-0.2525	-0.1262	0.1417	0.1774	-0.1301	-0.2822	0.0557	0.0326	0.3035	-0.0354	-0.065	0.5477	-0.062	0.3091	5.4575	94.8616	48.3001
32	0.1656	0.0915	0.1009	0.0704	-0.0247	0.1755	0.1544	-0.0919	0.015	0.0312	0.0662	0.016	0.0322	0.2474	0.148	0.2563	-0.0234	0.0179	0.3252	-0.1163	0.3228	1.5484	106.5164	44.4732
33	0.0507	-0.0152	-0.0089	0.0444	0.0224	0.0094	0.0801	0.1833	0.0108	-0.0197	0.0006	-0.0393	-0.0023	0.063	0.0889	0.3135	-0.123	0.1052	0.3658	-0.4332	0.2131	0.1055	110.205	58.3385
34	0.0769	0.0194	0.0295	0.2052	0.006	0.0184	0.0615	-0.0572	0.0503	0.2134	-0.0348	0.1411	-0.209	-0.0709	0.2975	0.7885	-0.0408	-0.1345	0.8348	-0.3628	0.3827	-15.9566	108.9841	72.5597
35	0.0007	0.0003	0.0017	0.004	0.0059	0.0055	0.0657	0.0252	0.0137	-0.0453	0.0572	0.0441	-0.0193	-0.0047	0.0001	0.5991	-0.0062	0.0048	0.6592	-0.028	0.6164	-21.052	104.7998	63.7423
36	0.0063	-0.0113	-0.0108	0.0546	-0.0143	0.0392	-0.1129	-0.1505	-0.0232	-0.1274	-0.0321	0.0014	-0.0422	0.0947	-0.0326	0.4205	0.017	-0.0258	0.7322	-0.2501	0.4573	-18.0152	99.1011	74.4585
37	0.1348	-0.0055	0.0674	0.1014	0.036	0.4491	0.4082	-0.1269	-0.0493	0.0292	0.0908	-0.0923	-0.2953	0.104	0.6931	0.7024	-0.3398	-0.0885	0.6763	-0.51	0.4623	-16.7377	109.4833	74.4661
38	0.0073	0.0166	-0.0196	0.0284	-0.0284	0.03	0.1038	-0.0421	0.0883	0.0363	-0.0508	0.0803	-0.1873	0.0836	0.0655	0.5502	-0.0835	-0.2012	0.4024	-0.3421	0.8856	-9.7318	122.8703	53.2493
39	0.0159	-0.0222	0.0114	0.0767	-0.1069	0.1611	-0.0676	-0.1282	0.0008	0.1238	-0.0041	-0.0115	-0.0995	0.3542	-0.04	0.1906	0.1524	-0.2147	1.0583	0.0855	0.7166	15.1791	90.6739	63.9787
40	0.0275	-0.0209	0.0721	0.0309	-0.0648	0.2012	-0.2754	-0.1094	0.0414	-0.0342	0.1743	0.1661	-0.0762	-0.5099	-0.0645	0.2636	-0.0971	-0.0493	1.0544	-0.1871	0.5322	-22.3914	91.7036	63.5228
41	0.1753	-0.0139	-0.0219	-0.0071	0.0389	0.0985	-0.2025	-0.1073	-0.1788	-0.0612	-0.0371	0.0889	-0.0726	-0.1982	-0.3132	-0.1834	0.0353	-0.0103	0.9376	-0.3295	0.6545	-21.312	91.2567	61.1264
42	0.0279	-0.055	0.0035	0.0991	0.0342	0.0144	-0.2355	-0.0614	0.0494	0.068	-0.143	-0.1944	-0.0656	0.1006	-0.6883	0.1055	0.1148	-0.463	1.4156	-0.0983	0.8499	15.8341	90.247	64.7795

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 60 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 105 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 106 through 120 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 121 through 139 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 27 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 28 through 60 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 61 through 88 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 89 through 139 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 1 through 5 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 6 through 14 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 15 through 24 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 1 through 10 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 11 through 19 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 20 through 24 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 2 through 27 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 28 through 80 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 81 through 117 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 118 through 139 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 0 through 46 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 47 through 73 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 74 through 94 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 95 through 139 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 1 through 7 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 8 through 19 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 20 through 24 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 1 through 5 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 6 through 17 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 18 through 24 )
30	X-RAY DIFFRACTION	30	chain 'I' and (resid 2 through 27 )
31	X-RAY DIFFRACTION	31	chain 'I' and (resid 28 through 80 )
32	X-RAY DIFFRACTION	32	chain 'I' and (resid 81 through 138 )
33	X-RAY DIFFRACTION	33	chain 'J' and (resid 0 through 27 )
34	X-RAY DIFFRACTION	34	chain 'J' and (resid 28 through 49 )
35	X-RAY DIFFRACTION	35	chain 'J' and (resid 50 through 60 )
36	X-RAY DIFFRACTION	36	chain 'J' and (resid 61 through 81 )
37	X-RAY DIFFRACTION	37	chain 'J' and (resid 82 through 116 )
38	X-RAY DIFFRACTION	38	chain 'J' and (resid 117 through 139 )
39	X-RAY DIFFRACTION	39	chain 'K' and (resid 1 through 10 )
40	X-RAY DIFFRACTION	40	chain 'K' and (resid 11 through 24 )
41	X-RAY DIFFRACTION	41	chain 'L' and (resid 1 through 14 )
42	X-RAY DIFFRACTION	42	chain 'L' and (resid 15 through 24 )

-
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