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

ID or keywords:

Entry

Database: PDB / ID: 4lll

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/SAD / Resolution: 3.036 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	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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	4lll.cif.gz	576.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4lll.ent.gz	475.9 KB	Display	PDB format
PDBx/mmJSON format	4lll.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4lll_validation.pdf.gz	517.9 KB	Display	wwPDB validaton report
Full document	4lll_full_validation.pdf.gz	560.2 KB	Display
Data in XML	4lll_validation.xml.gz	45.2 KB	Display
Data in CIF	4lll_validation.cif.gz	62.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ll/4lll ftp://data.pdbj.org/pub/pdb/validation_reports/ll/4lll	HTTPS FTP

-
Related structure data

Related structure data	4llnC C: citing same article (ref.)
Similar structure data	4lln-1 4lln-2 4lln-3 1y1a-d 3q5f-d 5hlh-4 2emt-2 5oy3-d 4xhu-2 5hux-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) 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

4llnC

C: citing same article (ref.)

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

C: MepR

D: MepR

I: MepR

J: MepR

M: MepR

O: MepR

E: Palindromized mepR operator sequence

F: Palindromized mepR operator sequence

G: Palindromized mepR operator sequence

H: Palindromized mepR operator sequence

K: Palindromized mepR operator sequence

L: Palindromized mepR operator sequence

174 kDa, 14 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)

4

M: MepR

O: MepR

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

Unit cell

Length a, b, c (Å)	130.177, 130.177, 124.707
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	MepR Mass: 16262.288 Da / Num. of mol.: 8 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 / Source method: obtained synthetically

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 64.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.04M Mg Acetate, 0.05M Na Cacodylate, 30% (+/-)-2-methyl-2,4-pentanediol., pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	5.0.2	1	1
SYNCHROTRON	ALS	5.0.2	2	0.979

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315r	1	CCD	Jul 18, 2012
ADSC QUANTUM 315r	2	CCD	Jul 18, 2012

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double-crystal, Si(111) liquid N2 cooled	SINGLE WAVELENGTH	M	x-ray	1
2	Double-crystal, Si(111) liquid N2 cooled	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.979	1

Reflection

Resolution: 3→50 Å / Num. all: 47910 / Num. obs: 47910 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 11.5 % / B_iso Wilson estimate: 79.47 Å² / R_merge(I) obs: 0.081 / Net I/σ(I): 42.9

-
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/SAD / Resolution: 3.036→42.61 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.41 / σ(F): 1.97 / Phase error: 25.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.234	1929	4.24 %
R_work	0.1936	-	-
obs	0.1952	45454	99.58 %
all	-	45646	-

Solvent computation

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

Displacement parameters

B_iso mean: 75.2658 Å²

Refinement step

Cycle: LAST / Resolution: 3.036→42.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8103	2934	0	0	11037

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11494
X-RAY DIFFRACTION	f_angle_d	1.533	16182
X-RAY DIFFRACTION	f_dihedral_angle_d	22.762	4291
X-RAY DIFFRACTION	f_chiral_restr	0.079	1887
X-RAY DIFFRACTION	f_plane_restr	0.005	1592

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 (%)
3.0358-3.1117	0.378	134	0.3133	3029	X-RAY DIFFRACTION	97
3.1117-3.1958	0.2597	144	0.249	3078	X-RAY DIFFRACTION	100
3.1958-3.2898	0.2614	134	0.2061	3039	X-RAY DIFFRACTION	99
3.2898-3.396	0.2815	140	0.2116	3180	X-RAY DIFFRACTION	100
3.396-3.5173	0.2467	140	0.2129	3152	X-RAY DIFFRACTION	100
3.5173-3.658	0.2614	134	0.2062	3075	X-RAY DIFFRACTION	100
3.658-3.8244	0.2377	144	0.2068	3140	X-RAY DIFFRACTION	100
3.8244-4.0259	0.2927	136	0.1905	3126	X-RAY DIFFRACTION	100
4.0259-4.2779	0.2279	141	0.183	3085	X-RAY DIFFRACTION	100
4.2779-4.6079	0.2283	138	0.1773	3158	X-RAY DIFFRACTION	100
4.6079-5.0709	0.2279	142	0.1916	3083	X-RAY DIFFRACTION	100
5.0709-5.8031	0.2573	125	0.2126	3137	X-RAY DIFFRACTION	100
5.8031-7.3053	0.2666	142	0.2139	3129	X-RAY DIFFRACTION	100
7.3053-42.6146	0.1671	135	0.1582	3114	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	8.275	-0.7144	4.1585	5.9325	-1.1881	6.6969	-0.3658	0.6584	0.4843	0.0364	-0.2224	0.2089	-0.8515	0.0018	0.4961	0.3731	0.1696	-0.0531	0.4561	-0.1123	0.4041	108.5569	89.6772	43.9719
2	0.9367	0.9792	0.176	2.12	-0.7194	0.7778	0.1366	-0.9601	0.6727	0.5518	0.1468	-0.1822	-0.6025	0.3957	-0.3153	0.76	-0.0257	-0.1088	0.6022	-0.2612	0.2311	118.9209	84.0902	59.6521
3	2.7082	-0.1501	1.0207	0.4352	-0.0282	3.1241	0.2091	-0.1456	0.0013	0.2979	0.2028	0.0024	0.0176	-0.6016	-0.1337	0.4818	0.0244	0.0666	0.3999	-0.1616	0.3148	114.1311	70.2261	54.5265
4	2.664	1.6954	-1.9678	2.5767	-0.1585	2.2519	-0.2164	0.3258	-0.1947	-0.0504	0.1257	0.0739	0.6834	-0.7601	0.132	0.6098	-0.0415	0.1079	0.4411	-0.1155	0.2696	116.2223	68.8666	44.4071
5	1.5597	-0.8853	0.0767	0.5178	-0.2022	0.8383	-0.2443	-0.1976	0.0492	0.2213	-0.3407	0.0187	0.8002	-0.1365	0.4256	0.6395	0.0422	0.0679	0.2962	-0.1098	0.2954	124.7089	66.9437	52.7214
6	5.9501	-0.7345	3.6789	4.497	-1.1518	7.4765	-0.2219	-0.8023	0.7839	0.6911	0.2752	-0.0046	-0.2208	-1.0445	-0.034	0.4133	0.0898	0.0391	0.5185	-0.1129	0.3945	107.5	81.1119	59.2843
7	1.1416	0.6366	2.2152	6.4599	1.0794	4.41	-0.3366	0.4637	-0.9223	-0.7983	0.1466	1.28	0.7158	-1.9003	0.2529	0.5657	-0.3039	-0.0778	0.8085	0.0418	0.6907	95.73	79.4773	41.2274
8	3.0236	0.262	0.1785	5.0456	-0.5852	4.0763	-0.2272	0.1426	-0.3604	0.48	-0.1418	0.1788	0.2057	-0.4076	0.3009	0.6055	0.0744	-0.0118	0.6515	-0.1133	0.4421	108.3462	79.0116	38.9127
9	2.7033	0.0446	-0.2652	2.6381	-0.4128	3.3686	-0.1384	0.1905	0.1618	0.0102	-0.1446	-0.0692	-0.6534	-0.2846	0.2539	0.6684	0.177	-0.2566	0.4108	-0.1034	0.3721	118.4038	96.045	30.7853
10	6.0598	-0.1667	-0.2444	1.289	0.6454	7.7587	0.3397	-0.0054	0.9255	0.3724	-0.6502	-0.3541	-2.3363	0.4689	-0.1128	1.0243	-0.1023	-0.0661	0.554	0.1407	0.3545	125.5782	101.539	24.9743
11	3.6092	0.6071	-1.5475	4.0869	-0.5879	2.0918	0.2982	0.7479	1.4855	-0.0038	-0.1617	0.1588	-2.2565	0.0714	-0.1663	2.1555	-0.1467	0.2656	0.9179	0.5043	1.2245	125.5406	114.3618	33.4818
12	4.4701	-0.7512	-1.7619	2.7514	-0.8484	6.8279	0.3948	0.558	-0.1146	-0.0709	-0.2602	0.707	-0.655	-1.2152	0.0877	0.4784	0.1815	-0.2446	0.6542	-0.0962	0.5947	111.8548	91.6067	23.1444
13	3.0171	1.1646	-1.9706	8.8888	0.3258	1.6634	-0.0107	1.3645	0.2847	-0.604	0.0406	1.8938	-0.5212	-1.556	0.0124	0.4535	0.3856	0.0323	1.4515	-0.1044	0.8651	96.0723	88.7754	39.2843
14	1.848	0.2675	0.8442	2.8931	0.3295	4.3517	0.0181	-0.2119	-0.108	0.1562	0.1485	0.2505	0.7957	0.4316	-0.203	0.5024	-0.0219	-0.0508	0.6176	0.086	0.2371	72.541	99.7493	83.4378
15	7.8254	5.1127	-3.2313	8.4423	-3.9325	5.0901	0.8898	1.0468	-1.1502	1.1487	-1.4463	-2.0421	0.4096	1.319	0.8048	1.6686	0.8022	-0.0312	1.2456	0.2229	1.0097	81.0701	83.0891	71.7995
16	7.797	-3.3291	6.7101	2.5331	-2.6888	6.3829	-0.7283	-0.2237	0.2638	0.7078	0.0193	-0.6143	-0.5293	0.2689	0.5332	0.9254	-0.0279	0.1246	0.5145	0.0364	0.3693	72.5005	93.8214	67.6138
17	0.6374	0.1695	-0.7707	0.7769	-0.8016	1.746	-0.3248	-0.0022	-0.5339	-0.0643	-0.2239	0.0806	1.1196	-0.3527	-0.3157	1.345	-0.7941	0.3052	0.6527	0.1957	0.1971	55.5849	88.7606	59.1283
18	0.9481	0.201	-1.3513	2.4855	-1.3905	2.4543	0.3293	-0.1259	-0.1609	0.3778	-0.0914	-0.146	1.0065	-0.6937	-0.0921	0.8477	-0.3618	-0.057	0.671	0.124	0.3832	49.7276	93.2063	63.8916
19	0.9909	0.6143	-1.156	1.6777	-2.0121	2.798	0.0351	0.0261	-0.1921	-0.0411	0.2508	0.2213	0.5212	-0.5263	-0.2501	0.9403	-0.5173	-0.3463	1.1237	0.3904	0.5535	35.9113	86.1605	64.9831
20	0.6274	-0.0904	-0.1348	1.9229	1.6907	3.4677	0.0207	-0.247	-0.6451	-0.0967	0.4238	-0.338	0.7519	0.1947	-0.0737	1.0828	-0.2704	0.0326	0.388	0.0831	0.4476	62.3575	88.4552	54.9313
21	4.9876	-1.15	-5.1864	0.2984	1.3627	6.1672	0.0497	-0.1978	-0.8	0.3225	-0.5291	-0.2127	1.602	0.2561	0.4443	2.0527	-0.0616	0.213	0.5802	-0.0177	0.6808	71.8586	76.4751	72.1356
22	2.6082	1.1765	4.0601	0.6451	1.8512	6.3056	-0.2312	-0.1118	-0.0874	0.0384	-0.2254	-0.3293	-0.4591	-0.5445	0.2573	1.0253	-0.0629	0.3174	0.6346	-0.1759	0.5975	87.1017	51.0749	31.8506
23	0.6026	-0.1425	0.6116	3.1388	3.0333	4.3776	-0.2267	0.8518	0.3816	-0.7516	0.0239	-0.4652	0.8495	0.1195	0.1472	1.1981	0.1462	0.098	0.8576	0.371	0.5842	76.64	46.5165	16.0087
24	2.9433	-0.4671	2.2613	1.7961	-0.7577	2.4604	0.2722	0.4999	0.333	-0.0596	-0.254	-0.3822	-0.8315	1.3549	-0.0462	0.9379	-0.0923	0.1944	0.5446	0.0062	0.4536	81.4682	35.3447	21.3589
25	2.0249	1.673	0.5769	1.462	1.0286	3.9674	-0.1021	0.2671	0.2535	-0.4598	0.0419	0.1124	0.038	0.0832	0.0837	0.9021	0.0484	-0.1403	0.3308	0.0486	0.8037	74.165	30.9777	24.7009
26	1.7924	-0.9758	0.2609	3.3098	0.7869	0.3486	-0.0626	0.2068	0.5879	-0.625	-0.1957	-1.28	-0.2454	0.024	0.2393	1.3462	0.0561	-0.0805	0.3015	0.1011	0.7444	69.6168	17.1896	27.3322
27	3.5153	-0.8878	-1.8028	0.8621	-1.2555	7.8295	-0.1824	0.4783	0.2138	-0.1249	0.527	0.4048	1.1229	-0.3582	-0.362	1.0667	-0.2326	0.07	0.6084	0.0926	0.5961	73.1103	27.3228	19.2291
28	2.2376	0.0634	1.569	2.1501	0.344	6.2222	0.3272	0.4708	0.1462	-0.5962	0.4725	-0.3973	-0.3655	0.7689	-0.3731	1.1806	-0.1103	0.5773	0.8204	0.0127	0.5176	87.6584	42.0402	16.3725
29	2.5707	-2.0333	1.9727	5.3077	2.1381	5.2278	0.5012	0.9413	0.1109	-0.306	0.3961	-1.449	0.3177	1.6729	-0.6456	0.4186	0.279	-0.2489	1.2458	-0.3488	0.7153	99.102	40.2137	34.4595
30	3.2402	-0.6374	-2.3566	6.6567	2.66	6.3345	-0.992	0.3906	-0.8233	-0.4452	-0.2933	0.2275	0.7596	0.3501	1.2854	0.906	-0.3593	0.0773	0.7809	-0.0332	0.6386	85.5364	41.3785	39.3346
31	2.5533	-1.5398	-0.357	1.4323	-0.8025	2.1117	-0.0364	-0.1584	0.1368	0.1131	-0.4695	-0.669	-0.1042	0.7237	0.5135	1.0645	-0.2305	-0.0054	0.4979	0.0802	0.8045	79.9418	54.827	47.8709
32	9.5271	1.6474	4.9265	2.2594	1.9308	3.2948	0.2991	-1.0434	2.2875	0.7215	-0.333	-0.8427	-0.8775	-0.0035	0.201	1.5685	-0.5503	0.0587	0.7395	-0.1571	1.7686	81.972	68.423	47.2843
33	3.7302	1.5592	1.4229	2.7481	1.9259	1.4229	0.7387	-0.183	1.1713	0.3963	-0.4461	-0.3913	-0.6327	0.0309	-0.1579	1.579	-0.2474	0.4678	0.481	0.0247	0.8136	79.9745	61.9207	37.1677
34	1.3564	-1.5262	1.8369	4.0337	-3.4307	3.2901	-0.0279	-0.0497	-0.024	-0.0564	-0.2953	0.7302	0.6882	-0.3884	0.3291	0.9703	-0.2446	0.196	0.5441	-0.0268	0.6136	70.4438	57.9444	42.4369
35	4.4791	-5.1828	4.6827	6.9108	-5.9306	5.1838	0.0726	-0.0477	1.1848	0.3056	-0.6718	0.0918	-2.2516	-0.7091	0.4654	1.4792	0.0114	0.5274	0.6469	-0.2435	1.1889	70.7478	63.8814	50.0461
36	2.8548	-0.2778	-1.8225	3.1536	1.9344	5.4406	0.6368	-0.7255	0.5397	-0.2817	0.0792	-0.6775	-0.4606	0.8881	-0.5859	0.7494	-0.2595	0.0584	0.5858	-0.1038	0.812	88.2663	54.2382	45.8737
37	0.5796	0.7386	0.1283	1.0979	0.0472	0.0959	1.2118	0.6151	0.204	0.5063	-0.7493	0.2362	-1.0834	-0.841	-0.3862	1.309	0.3719	0.1921	1.0374	0.0442	0.9036	127.9125	106.7434	86.4038
38	7.2176	-0.0415	-1.5937	9.1771	2.7627	6.2589	0.3317	0.466	0.0907	-0.9094	-0.3509	-0.0995	-0.9318	-0.3681	0.0516	0.874	0.134	-0.0461	0.439	-0.0203	0.4164	116.7356	85.1183	90.0767
39	2.8954	1.0662	-0.0348	5.1006	-1.2771	1.4723	0.3239	0.186	0.3941	0.5505	-0.2178	-0.185	-1.0496	-0.6798	0.1132	0.951	0.0276	0.1895	0.5129	-0.0917	0.489	112.662	88.2807	95.9384
40	0.2362	-0.1459	0.3337	1.7166	-1.451	1.4217	-0.1514	0.5121	0.9528	0.0332	-0.037	0.549	-0.6126	-0.3381	0.2054	1.4971	0.881	-0.2254	1.4252	0.3751	1.6	115.6257	116.2287	73.9819
41	1.0583	-1.0246	-0.1948	1.8532	0.81	0.4621	-0.3412	0.6149	-0.3223	0.0808	0.3017	0.59	-1.0021	-0.077	0.1613	1.0178	-0.0005	0.2174	0.9304	0.0833	0.7083	125.4969	104.6737	71.1661
42	5.8248	1.3387	-1.9254	5.3114	-1.4305	8.5991	-0.3453	-1.5142	0.5961	0.5882	-0.0554	-0.0623	0.5426	1.3885	0.2595	0.8319	-0.065	0.0176	1.1091	-0.0901	0.4658	148.6571	104.6719	71.7151
43	7.224	-0.3543	3.0503	0.2133	-0.3418	2.0416	-0.1301	-0.3855	0.0442	0.1779	-0.2857	-0.1405	0.255	0.57	0.2022	0.7698	-0.1877	-0.1351	1.1031	-0.1509	0.3876	155.4926	99.1814	66.8114
44	0.6929	0.0142	0.6058	1.952	0.2595	0.5516	0.0776	0.1473	0.6639	0.8095	1.2752	0.6199	-1.5804	-1.8885	-0.9433	1.0668	0.5032	0.1651	1.4634	0.2758	0.6516	134.83	111.5795	62.5083
45	4.6742	-1.2644	-2.3779	0.3416	0.6424	1.2087	1.5506	1.225	1.3868	-0.713	-0.3998	0.4837	-1.7249	-0.5255	-1.0128	2.6196	0.2873	0.8149	0.789	0.2353	1.3863	123.5832	122.1888	80.0369
46	2.4883	1.5344	0.9021	2.9251	0.7061	2.2968	-0.3214	-0.2815	0.6566	-0.6382	0.0793	0.4288	0.1994	-0.9373	-0.1571	0.2865	-0.5765	-0.0681	0.9627	0.1844	0.3962	57.3705	105.5742	72.2869
47	5.3251	2.2143	-0.2072	2.4486	-0.0354	2.8865	-0.3905	-0.3373	0.8576	-0.2518	0.0181	0.6154	0.1921	-0.4769	-0.2436	0.452	-0.435	-0.0229	0.8069	0.2007	0.343	58.4025	106.0429	73.2565
48	2.8627	-2.191	0.4129	1.6708	-0.387	0.0968	-0.2425	0.5876	-0.0916	-1.0283	-0.4122	-0.7986	1.0384	0.0277	-0.2645	1.0893	0.0834	0.2518	0.3013	-0.1461	0.3962	127.5671	69.0501	37.3744
49	2.1491	-1.3631	-0.281	2.9493	-0.8484	0.5795	0.2028	0.4505	1.1755	-0.6102	-0.6979	-0.9819	-1.1093	0.2234	0.127	1.2161	0.0161	-0.1698	0.3775	0.0888	0.8262	128.8274	104.656	44.9642
50	1.6546	-0.2758	-0.6431	1.2174	-0.6322	1.5926	-0.0519	-0.0744	0.7471	0.3047	-0.3638	-0.1916	-0.8302	-0.1003	0.3044	1.0551	0.0699	-0.1314	0.3132	-0.0659	0.7279	129.3788	104.5737	45.1411
51	0.2906	-0.8588	0.0892	2.3894	-0.1612	0.5553	0.034	0.2818	-0.4634	-0.7152	-0.6462	-0.4047	1.1148	0.0527	-0.2781	1.3254	0.3047	0.2825	0.1672	-0.2069	0.5569	127.5929	67.5219	38.815
52	0.9237	0.1209	0.0276	0.1386	0.4363	1.1955	0.6629	-0.0345	0.3971	-0.1282	-0.5703	1.239	-0.469	-0.0989	-0.0892	1.5689	0.0892	0.2328	0.32	0.1031	1.2131	67.5561	47.4885	34.4433
53	1.3217	-0.1006	0.6633	0.4014	0.5851	1.3392	0.6592	-0.3851	0.333	0.1458	-0.3942	1.3119	-0.3279	-0.1589	-0.122	1.309	0.0017	0.2636	0.3106	0.0058	1.147	67.3903	46.5121	33.5041

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 49 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 50 through 60 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 94 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 95 through 118 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 119 through 139 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 23 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 24 through 73 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 74 through 81 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 82 through 88 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 89 through 117 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 118 through 139 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 2 through 120 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 121 through 139 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 3 through 27 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 28 through 49 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 50 through 81 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 82 through 88 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 89 through 118 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 119 through 139 )
22	X-RAY DIFFRACTION	22	chain 'I' and (resid 3 through 24 )
23	X-RAY DIFFRACTION	23	chain 'I' and (resid 25 through 30 )
24	X-RAY DIFFRACTION	24	chain 'I' and (resid 31 through 43 )
25	X-RAY DIFFRACTION	25	chain 'I' and (resid 44 through 81 )
26	X-RAY DIFFRACTION	26	chain 'I' and (resid 82 through 88 )
27	X-RAY DIFFRACTION	27	chain 'I' and (resid 89 through 94 )
28	X-RAY DIFFRACTION	28	chain 'I' and (resid 95 through 118 )
29	X-RAY DIFFRACTION	29	chain 'I' and (resid 119 through 139 )
30	X-RAY DIFFRACTION	30	chain 'J' and (resid 2 through 27 )
31	X-RAY DIFFRACTION	31	chain 'J' and (resid 28 through 42 )
32	X-RAY DIFFRACTION	32	chain 'J' and (resid 43 through 49 )
33	X-RAY DIFFRACTION	33	chain 'J' and (resid 50 through 60 )
34	X-RAY DIFFRACTION	34	chain 'J' and (resid 61 through 73 )
35	X-RAY DIFFRACTION	35	chain 'J' and (resid 74 through 81 )
36	X-RAY DIFFRACTION	36	chain 'J' and (resid 82 through 139 )
37	X-RAY DIFFRACTION	37	chain 'M' and (resid 6 through 26 )
38	X-RAY DIFFRACTION	38	chain 'M' and (resid 27 through 73 )
39	X-RAY DIFFRACTION	39	chain 'M' and (resid 74 through 113 )
40	X-RAY DIFFRACTION	40	chain 'M' and (resid 114 through 139 )
41	X-RAY DIFFRACTION	41	chain 'O' and (resid 5 through 27 )
42	X-RAY DIFFRACTION	42	chain 'O' and (resid 28 through 60 )
43	X-RAY DIFFRACTION	43	chain 'O' and (resid 61 through 94 )
44	X-RAY DIFFRACTION	44	chain 'O' and (resid 95 through 118 )
45	X-RAY DIFFRACTION	45	chain 'O' and (resid 119 through 139 )
46	X-RAY DIFFRACTION	46	chain 'E' and (resid 1 through 24 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 1 through 24 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 1 through 13 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 14 through 24 )
50	X-RAY DIFFRACTION	50	chain 'H' and (resid 1 through 11 )
51	X-RAY DIFFRACTION	51	chain 'H' and (resid 12 through 24 )
52	X-RAY DIFFRACTION	52	chain 'K' and (resid 1 through 24 )
53	X-RAY DIFFRACTION	53	chain 'L' and (resid 1 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