PDB-5d8c: Crystal structure of HiNmlR, a MerR family regulator lacking the ...

ID or keywords:

Entry

Database: PDB / ID: 5d8c

Title

Crystal structure of HiNmlR, a MerR family regulator lacking the sensor domain, bound to promoter DNA

Components

DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*AP*AP*CP*TP*CP*TP*AP*AP*G)-3')
DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*TP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3')
MerR family regulator protein

Keywords

transcription/dna / Transcription factor / MerR / thiol-based genetic switch / DNA untwisting / transcription-dna complex

Function / homology

Function and homology information

DNA-binding transcription factor activity / DNA binding
Similarity search - Function

Biological species

Haemophilus influenzae (bacteria)

Haemophilus influenzae Rd KW20 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Counago, R.M. / Chang, C.W. / Chen, N.H. / Djoko, K.Y. / McEwan, A.G. / Kobe, B.

Funding support

Australia, 3items

Organization	Grant number	Country
Australian Research Council (ARC)	DP0986578	Australia
National Health and Medical Research Council (NHMRC, Australia)	565526	Australia
National Health and Medical Research Council (NHMRC, Australia)	1071659	Australia

Citation

Journal: Nucleic Acids Res. / Year: 2016
Title: Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region.
Authors: Counago, R.M. / Chen, N.H. / Chang, C.W. / Djoko, K.Y. / McEwan, A.G. / Kobe, B.

History

Deposition	Aug 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 31, 2016	Group: Database references
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5d8c.cif.gz	167 KB	Display	PDBx/mmCIF format
PDB format	pdb5d8c.ent.gz	131.9 KB	Display	PDB format
PDBx/mmJSON format	5d8c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5d8c_validation.pdf.gz	438 KB	Display	wwPDB validaton report
Full document	5d8c_full_validation.pdf.gz	438.4 KB	Display
Data in XML	5d8c_validation.xml.gz	14.2 KB	Display
Data in CIF	5d8c_validation.cif.gz	21 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8c ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8c	HTTPS FTP

-
Related structure data

Related structure data	5d90C 5e01C 3gpvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5e01-d 3mml-5 3fzl-d 5l2w-d 6kgf-d 5aqr-2 5aqp-3 5aqq-3 6lki-d 1zvm-5 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (2) #168 - Dec 2013 DNA Helicase 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) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (2)
#168 - Dec 2013
DNA Helicase
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)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)

Deposited unit

A: MerR family regulator protein

B: MerR family regulator protein

C: DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*TP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3')

D: DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*AP*AP*CP*TP*CP*TP*AP*AP*G)-3')

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.030, 111.820, 103.170
Angle α, β, γ (deg.)	90.00, 102.10, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	MerR family regulator protein Mass: 15687.036 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: HI_0186 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21De(3) / References: UniProt: P44558
#2: DNA chain	DNA (5'-D(CPTPTPAPGPAPGPTPTPCPAPCPTPCPTPAPAPG)-3') Mass: 5490.578 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Promoter sequence for adhC-estD operon and nmlR gene. Source: (synth.) Haemophilus influenzae Rd KW20 (bacteria)
#3: DNA chain	DNA (5'-D(CPTPTPAPGPAPGPTPGPAPAPCPTPCPTPAPAPG)-3') Mass: 5539.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae Rd KW20 (bacteria)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.73 Å³/Da / Density % sol: 66.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% w/v PEG 3,350; 0.4 M sodium nitrate; 0.1 M Bis-Tris propane; 2 mM TCEP

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 13, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.25→37.45 Å / Num. obs: 22051 / B_iso Wilson estimate: 61.58 Å²
Reflection shell	Resolution: 2.25→2.33 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.675 / Mean I/σ(I) obs: 1.1 / % possible all: 14.3

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.1	refinement
XDS		data reduction
Aimless		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3gpv

3gpv

Resolution: 2.25→37.45 Å / Cor.coef. F_o:F_c: 0.9442 / Cor.coef. F_o:F_c free: 0.9226 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.307 / SU R_free Blow DPI: 0.229 / SU R_free Cruickshank DPI: 0.222

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2438	1147	5.2 %	RANDOM
R_work	0.2076	-	-	-
obs	0.2095	22051	74.76 %	-

Displacement parameters

B_iso mean: 60.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.5977 Å²	0 Å²	-2.3004 Å²
2-	-	1.0718 Å²	0 Å²
3-	-	-	-0.4742 Å²

Refine analyze

Luzzati coordinate error obs: 0.436 Å

Refinement step

Cycle: LAST / Resolution: 2.25→37.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2049	738	0	241	3028

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	2903	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.02	4056	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1194	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		55	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		328	HARMONIC	5
X-RAY DIFFRACTION	t_it		2903	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.99
X-RAY DIFFRACTION	t_other_torsion	3.74
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		380	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		3340	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.25→2.36 Å / Total num. of bins used: 11

	R_factor	Num. reflection	% reflection
R_free	0.2994	27	4.29 %
R_work	0.2762	603	-
all	0.2772	630	-
obs	-	-	74.76 %

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	-0.2592	1.8699	0.269	0.0012	-1.5791	3.5764	0.0009	0.1583	0.036	-0.1354	-0.0536	0.2299	-0.0141	-0.0529	0.0527	0.0181	-0.0893	-0.0844	0.2913	0.0673	-0.3394	-7.6006	-39.6119	107.7793
2	0.8789	1.1157	-1.6013	0	-0.655	-0.4003	0.0054	0.0715	-0.015	-0.1477	0.0104	0.1734	-0.0282	-0.0056	-0.0159	0.1865	0.0581	0.0373	0.2697	0.1378	-0.2947	-7.1313	-32.9493	112.7562
3	-0.7632	3.231	1.5943	0	-1.5272	1.7322	0.0101	0.1956	0.0156	-0.1696	-0.1351	0.0438	0.1471	-0.1219	0.125	0.1687	-0.1522	0.0943	0.2521	-0.015	-0.2477	2.7831	-35.2984	114.6864
4	1.2433	0.2935	-2.8891	0.0278	-2.8426	-0.0995	0.0096	0.1109	-0.087	-0.032	0.1363	-0.1384	0.1063	0.0813	-0.1459	0.0883	-0.1278	0.087	0.0502	-0.0666	-0.2409	3.6266	-40.6468	119.9931
5	2.0569	0.3775	-0.0973	0.123	0.6894	1.5013	-0.0165	-0.0472	-0.0875	-0.077	0.0022	-0.0042	0.2698	0.0818	0.0143	0.1672	-0.1581	-0.0287	-0.1416	0.0124	-0.1824	-2.3001	-45.9884	118.8248
6	0.787	-0.191	0.6921	0.7848	1.1751	0.6571	0.0154	0.0429	-0.0424	-0.0364	-0.0396	0.0141	0.0292	-0.0338	0.0242	0.327	-0.1191	0.0098	0.298	-0.1693	-0.3288	0.6523	-49.1065	104.2693
7	-0.2631	-0.082	0.495	0	-1.1371	1.1513	0.0189	0.0642	-0.0483	-0.0866	-0.0581	0.1014	-0.0053	-0.01	0.0392	0.1457	-0.1182	-0.0576	0.211	-0.1736	-0.3326	-2.6552	-44.1742	108.7444
8	0.3548	0.325	-0.8256	0.4914	1.1489	0.2336	0.0224	0.1224	0.0058	-0.0219	0.0035	0.0286	-0.1059	-0.0731	-0.0259	0.039	-0.1692	-0.0973	0.1434	0.0667	-0.2132	-10.8075	-44.0797	115.3073
9	1.3156	1.4138	-3.3467	0.0241	1.7035	2.5968	0.0681	0.0797	-0.0257	-0.1035	-0.0431	0.022	-0.0781	-0.1343	-0.0249	0.0303	-0.1798	0.0534	0.1159	0.1135	-0.1542	-8.8344	-38.9491	122.5109
10	0.0648	2.2304	-0.1801	0	2.8452	0.3532	0.1106	0.137	0.1018	0.0851	0.1918	0.0892	-0.3647	-0.0019	-0.3024	0.0499	-0.1697	0.0588	-0.0054	0.0663	-0.0805	-4.5947	-33.6607	129.3823
11	1.2645	-0.5944	1.1436	0.0001	2.8472	0.9009	0.1007	0.0267	-0.1201	-0.1493	-0.0524	0.0459	-0.0934	0.1193	-0.0483	-0.0023	-0.1585	0.0332	0.2098	0.0223	-0.1191	1.146	-42.1492	130.8871
12	0.1303	-1.938	-0.29	1.3126	1.2642	-0.1303	0.0234	0.0501	-0.3311	0.0236	-0.0069	-0.0385	-0.0039	-0.1372	-0.0166	0.2287	-0.1253	0.1336	-0.0934	0.0097	-0.061	-3.2533	-49.5118	128.4641
13	1.7099	0.7855	-0.9014	2.0259	0.0275	-0.3779	-0.0095	-0.1555	-0.0925	0.0052	-0.0214	-0.0156	0.1446	-0.0453	0.0309	0.2031	-0.1803	0.1122	-0.2492	0.1168	0.127	-7.9994	-53.5453	135.3093
14	-0.0012	2.1997	-0.1765	1.0979	1.9584	1.6732	-0.0477	-0.1103	-0.086	-0.0047	-0.0545	0.0995	0.0255	-0.2797	0.1022	0.0295	-0.1747	0.0229	0.0641	0.0972	-0.1014	-9.2158	-44.5883	136.5949
15	1.2748	1.0027	-2.0543	1.7003	3.1132	2.0036	-0.0475	-0.0759	0.0884	0.0116	0.1465	0.0323	0.0643	-0.1441	-0.099	-0.051	-0.1604	-0.0563	0.1568	0.0233	-0.05	-10.5961	-34.6388	138.8834
16	1.0592	0.3389	-2.4464	2.3438	2.9327	-0.1869	-0.0965	0.0698	0.0997	0.172	0.0005	0.0169	0.1851	0.2262	0.096	-0.1123	-0.0885	-0.0234	0.1479	0.042	-0.1481	-12.4595	-26.2686	139.4289
17	1.193	2.3678	-2.6546	0	2.8396	-1.193	-0.0305	-0.0618	-0.0321	0.0601	-0.0413	0.0044	-0.1147	0.0295	0.0718	-0.0534	-0.0234	-0.0395	0.1573	-0.0105	-0.0543	-12.5773	-15.9274	139.1398
18	1.3439	0.2517	-0.0247	0.5909	0.5719	-0.0723	0.0609	0.0752	-0.0894	0.0458	-0.0404	0.1509	-0.1534	0.085	-0.0205	-0.2434	-0.0345	-0.1062	0.1457	0.0717	-0.123	-13.4486	-5.7091	137.108
19	2.1489	-1.0375	-1.346	1.0401	0.1082	-0.6759	0.0509	-0.0893	0.0411	-0.0481	-0.0004	0.0879	-0.2432	0.1319	-0.0505	0.0908	0.0441	-0.1519	-0.1286	0.0508	0.2208	-12.7891	1.9722	133.8621
20	1.3233	-1.2933	-1.2712	1.9322	0.2264	-0.5971	0.0343	0.0996	0.1174	-0.0659	-0.0633	0.0048	-0.1373	-0.0743	0.029	0.1294	-0.1793	-0.1884	-0.3036	0.1111	0.2262	-9.324	7.7569	137.6139
21	2.1057	3.3247	-2.7409	5.223	-2.0139	1.0217	-0.0325	-0.1102	0.1116	0.0614	-0.0154	-0.0159	-0.1048	-0.0764	0.0479	-0.053	-0.0282	-0.1138	0.1327	-0.1096	0.0748	6.4149	-8.1025	154.536
22	1.038	3.23	1.1989	0	-2.2659	2.1543	-0.091	-0.0581	-0.0028	0.0137	0.1315	0.1294	0.0744	0.0472	-0.0406	-0.1198	0.0483	-0.0022	0.1047	-0.0012	-0.0258	5.2925	-16.5376	150.8805
23	0.4991	-1.6475	-0.1235	0.4682	1.6343	8.6217	-0.0724	-0.2789	0.1723	-0.367	-0.1061	-0.0448	-0.0256	0.1511	0.1785	-0.0798	-0.0507	-0.0616	0.1169	-0.0233	0.0416	11.1595	-17.4333	142.3518
24	-0.6844	-0.5644	2.1561	1.6979	-2.9648	0.9559	0.0651	0.033	-0.2207	-0.1105	0.0853	-0.0532	-0.384	0.114	-0.1504	-0.017	-0.1522	-0.057	0.1403	-0.0153	-0.007	10.3359	-11.0209	136.5933
25	1.2639	-1.2339	-2.9853	0.8015	0.1075	0.3494	-0.0172	-0.1565	0.1277	0.0804	-0.0535	-0.0191	-0.269	-0.0384	0.0707	-0.0431	-0.1332	-0.0285	-0.0856	0.016	-0.0198	10.0794	-4.1037	143.2749
26	0.0401	1.3316	0.8898	0.5966	-0.6095	0.3798	-0.0236	-0.164	0.1306	0.056	0.0519	-0.1305	-0.0465	0.1169	-0.0283	-0.1162	0.0046	-0.1304	0.1344	-0.0522	0.0607	19.397	-4.4553	152.6422
27	0.4608	1.6408	-1.0508	0.0264	1.6816	-0.2238	0.0077	-0.0616	0.0889	0.0984	-0.0187	0.054	-0.129	0.0981	0.011	-0.1374	-0.1071	-0.0858	-0.1322	-0.0192	0.0382	10.2079	-7.4076	149.4163
28	0.6787	2.4289	-1.417	0	2.4048	0.082	-0.1183	-0.2376	0.1752	-0.1414	0.1889	0.2596	0.0951	-0.086	-0.0706	-0.0133	-0.0015	-0.014	0.056	0.0656	0.0345	0.2782	-7.7438	144.6131
29	-0.9423	0.6437	1.5875	1.8306	-0.9677	5.692	0.0489	-0.0392	-0.2114	-0.134	-0.0658	0.0133	-0.0357	-0.293	0.0169	0.0013	-0.1533	-0.046	0.0949	0.0873	0.1401	-1.747	-15.1601	137.4086
30	0.1935	-0.0699	-0.5086	0.5189	2.895	0.5346	0.0769	0.0587	-0.1155	-0.2257	-0.0419	0.2182	-0.1417	0.0133	-0.0349	-0.0852	-0.1354	-0.0911	-0.0861	0.0331	-0.0529	-1.3901	-16.4384	132.1404
31	-0.1115	1.6017	0.248	0.0068	1.7295	0.1115	-0.0012	0.1297	0.2538	-0.3628	0.0178	-0.1836	-0.0063	-0.0794	-0.0166	0.0978	-0.1229	-0.0735	0.0652	0.0728	-0.0304	2.5207	-7.6149	130.065
32	-1.19	2.738	2.6406	0.0171	-2.1943	1.2584	0.0288	-0.0515	0.1861	-0.2224	-0.0516	-0.1078	-0.2883	-0.1543	0.0228	0.004	-0.1605	-0.1103	-0.1388	0.121	0.0448	1.4951	1.9691	132.5922
33	-1.0554	-0.1019	2.6272	0.5991	-1.0317	1.1848	-0.0142	0.0304	0.1654	-0.0324	-0.0106	0.055	-0.0528	-0.0126	0.0247	0.3501	-0.0787	-0.101	-0.2429	0.1386	0.0579	-5.0597	2.3318	127.7915
34	-0.4057	0.6973	0.7326	0	-2.2395	1.9934	0.0718	0.0361	-0.0164	-0.1276	-0.0423	0.283	-0.0631	-0.1814	-0.0295	-0.0437	-0.0222	-0.1944	-0.0441	0.1152	0.0799	-8.7182	-4.7727	129.7992
35	-0.1976	1.3653	2.1294	0.1238	-2.467	0.9221	0.0417	0.0053	-0.026	-0.0563	0.0101	-0.0334	-0.2088	-0.0594	-0.0519	-0.1154	-0.1547	-0.1102	0.1197	0.035	-0.1276	-11.7292	-13.8315	128.7272
36	2.5972	0.7883	-0.462	1.7863	3.1455	-0.3175	-0.1247	-0.0107	-0.0382	-0.2317	0.0475	0.1621	0.205	-0.1633	0.0772	-0.05	-0.1682	-0.1284	0.2213	0.0594	-0.0881	-15.559	-23.2038	130.3076
37	-1.1879	1.3099	2.6454	0.6844	-0.9033	1.1888	-0.0276	0.1282	0.2231	-0.0167	0.0163	0.0496	0.0374	-0.0256	0.0113	-0.0679	-0.1618	-0.0327	0.034	0.0297	0.0008	-16.1552	-33.507	129.7297
38	2.0012	2.7768	-2.4814	0.5505	0.7264	-1.1559	0.0714	0.0628	-0.1708	-0.0809	-0.0453	0.1113	0.0024	-0.0838	-0.026	-0.1239	-0.1724	-0.0423	0.0235	0.0794	0.1346	-17.7948	-41.6874	132.7113
39	1.1084	3.4407	-2.4663	0.4004	-2.2086	-1.1084	-0.0122	-0.0886	-0.0137	0.0001	0.0547	0.1495	0.1273	0.3444	-0.0425	0.0363	-0.1776	-0.0189	-0.0648	0.1036	-0.0049	-16.5449	-49.7777	135.1085
40	6.9151	3.1796	-1.3065	1.0483	-0.9471	-0.8418	0.054	-0.1728	-0.1704	-0.0348	-0.1404	-0.0501	0.0424	-0.095	0.0864	0.0491	-0.1805	-0.0215	-0.0998	0.1167	0.1146	-16.7931	-55.5718	130.1555
41	7.9526	2.0944	1.0595	5.4775	3.4251	1.618	-0.0174	0.3031	0.0435	-0.3866	0.2541	0.0941	0.0762	0.1039	-0.2367	-0.0918	-0.1402	-0.0446	0.2364	-0.0709	-0.1435	20.8994	-13.3521	143.8948
42	3.8828	2.2357	1.6456	3.8404	3.4558	9.2077	0.0912	-0.2254	-0.4728	-0.4525	0.2141	-0.4855	0.25	0.491	-0.3053	-0.1161	-0.1015	0.0064	0.297	-0.1772	0.0235	17.6705	-25.3097	132.0876
43	5.9991	1.9344	-0.2522	2.0271	-2.3335	2.0751	0.1167	0.2369	0.1068	-0.5979	0.1579	0.1927	-0.3877	0.0415	-0.2746	0.0839	-0.1496	0.102	0.0401	-0.027	-0.278	6.7085	-29.7641	118.8916
44	0.5915	3.2904	-2.1076	0.3859	-1.5218	6.793	0.1317	0.4647	0.1621	-0.1542	0.0649	-0.5897	0.0727	0.4046	-0.1966	0.2594	-0.1201	0.1644	0.304	-0.165	-0.2594	14.4932	-35.3444	105.3002
45	7.9565	2.965	-2.9697	6.7885	-0.5348	7.0586	0.0478	-0.0066	-0.2646	-0.1704	-0.0004	-0.1151	-0.1544	-0.1417	-0.0474	0.3397	-0.1169	-0.0146	0.3	-0.0842	-0.3369	8.2917	-40.344	108.6234
46	4.2831	2.1907	1.1357	1.3386	2.887	6.6472	0.1122	0.4281	0.1531	-0.0866	-0.121	-0.555	0.0787	0.5996	0.0088	-0.0532	-0.1167	0.1161	0.2827	-0.1805	-0.1773	15.5746	-30.9035	117.1975
47	3.2894	-2.2696	-0.7361	3.8795	-3.2974	1.5892	-0.0357	0.5746	-0.4368	-0.5614	0.2064	0.1712	-0.1171	-0.084	-0.1707	-0.0963	-0.14	-0.0653	-0.0731	-0.072	-0.2293	10.338	-21.8664	130.6578
48	6.5923	-2.7234	4.2801	8.3155	-1.1809	1.5322	-0.0344	-0.3099	-0.533	-0.1447	0.1253	-0.5606	0.4117	0.4902	-0.0908	-0.2912	-0.0406	-0.0412	0.304	-0.1641	-0.1705	25.3079	-20.3001	143.092

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|1 - 9}
2	X-RAY DIFFRACTION	2	{A\|10 - 15}
3	X-RAY DIFFRACTION	3	{A\|16 - 21}
4	X-RAY DIFFRACTION	4	{A\|22 - 26}
5	X-RAY DIFFRACTION	5	{A\|27 - 32}
6	X-RAY DIFFRACTION	6	{A\|33 - 37}
7	X-RAY DIFFRACTION	7	{A\|38 - 41}
8	X-RAY DIFFRACTION	8	{A\|42 - 46}
9	X-RAY DIFFRACTION	9	{A\|47 - 53}
10	X-RAY DIFFRACTION	10	{A\|54 - 62}
11	X-RAY DIFFRACTION	11	{A\|63 - 67}
12	X-RAY DIFFRACTION	12	{A\|68 - 75}
13	X-RAY DIFFRACTION	13	{A\|76 - 80}
14	X-RAY DIFFRACTION	14	{A\|81 - 87}
15	X-RAY DIFFRACTION	15	{A\|88 - 93}
16	X-RAY DIFFRACTION	16	{A\|94 - 99}
17	X-RAY DIFFRACTION	17	{A\|100 - 107}
18	X-RAY DIFFRACTION	18	{A\|108 - 112}
19	X-RAY DIFFRACTION	19	{A\|113 - 119}
20	X-RAY DIFFRACTION	20	{A\|120 - 126}
21	X-RAY DIFFRACTION	21	{B\|-1 - 5}
22	X-RAY DIFFRACTION	22	{B\|6 - 13}
23	X-RAY DIFFRACTION	23	{B\|14 - 21}
24	X-RAY DIFFRACTION	24	{B\|22 - 27}
25	X-RAY DIFFRACTION	25	{B\|28 - 33}
26	X-RAY DIFFRACTION	26	{B\|34 - 38}
27	X-RAY DIFFRACTION	27	{B\|39 - 42}
28	X-RAY DIFFRACTION	28	{B\|43 - 51}
29	X-RAY DIFFRACTION	29	{B\|52 - 56}
30	X-RAY DIFFRACTION	30	{B\|57 - 62}
31	X-RAY DIFFRACTION	31	{B\|63 - 69}
32	X-RAY DIFFRACTION	32	{B\|70 - 76}
33	X-RAY DIFFRACTION	33	{B\|77 - 81}
34	X-RAY DIFFRACTION	34	{B\|82 - 87}
35	X-RAY DIFFRACTION	35	{B\|88 - 93}
36	X-RAY DIFFRACTION	36	{B\|94 - 101}
37	X-RAY DIFFRACTION	37	{B\|102 - 107}
38	X-RAY DIFFRACTION	38	{B\|108 - 112}
39	X-RAY DIFFRACTION	39	{B\|113 - 119}
40	X-RAY DIFFRACTION	40	{B\|120 - 126}
41	X-RAY DIFFRACTION	41	{C\|1 - 4}
42	X-RAY DIFFRACTION	42	{C\|5 - 10}
43	X-RAY DIFFRACTION	43	{C\|11 - 14}
44	X-RAY DIFFRACTION	44	{C\|15 - 18}
45	X-RAY DIFFRACTION	45	{D\|1 - 4}
46	X-RAY DIFFRACTION	46	{D\|5 - 8}
47	X-RAY DIFFRACTION	47	{D\|9 - 13}
48	X-RAY DIFFRACTION	48	{D\|14 - 18}

-
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