PDB-9chl: P. vulgaris tetrameric HigBA- operator 2 DNA

ID or keywords:

Entry

Database: PDB / ID: 9chl

Title

P. vulgaris tetrameric HigBA- operator 2 DNA

Components

Antitoxin HigA
DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')
DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')
Endoribonuclease HigB

Keywords

ANTITOXIN/DNA BINDING PROTEIN/DNA / Toxin / antitoxin / promoter / DNA BINDING PROTEIN / ANTITOXIN-DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

toxin sequestering activity / plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / Hydrolases; Acting on ester bonds / transcription cis-regulatory region binding / negative regulation of translation ...
Similarity search - Function

Biological species

Proteus vulgaris (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Pavelich, I.J. / Schureck, M.A. / Hoffer, E.D. / Dunham, C.M.

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: P. vulgaris tetrameric HigBA- operator 2 DNA
Authors: Pavelich, I.J. / Schureck, M.A. / Hoffer, E.D. / Dunham, C.M.

History

Deposition	Jul 1, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9chl.cif.gz	424.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9chl.ent.gz	346.1 KB	Display	PDB format
PDBx/mmJSON format	9chl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9chl_validation.pdf.gz	466.4 KB	Display	wwPDB validaton report
Full document	9chl_full_validation.pdf.gz	469.3 KB	Display
Data in XML	9chl_validation.xml.gz	37.5 KB	Display
Data in CIF	9chl_validation.cif.gz	50 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ch/9chl ftp://data.pdbj.org/pub/pdb/validation_reports/ch/9chl	HTTPS FTP

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Related structure data

Related structure data	4mcxS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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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 (2) #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) #39 - Mar 2003 lac Repressor similarity (2) #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) #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 (6) #144 - Dec 2011 Complex I similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

A: Antitoxin HigA

B: Endoribonuclease HigB

C: Antitoxin HigA

D: Endoribonuclease HigB

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

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

E: Antitoxin HigA

F: Endoribonuclease HigB

G: Antitoxin HigA

H: Endoribonuclease HigB

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

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

hetero molecules

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

1

A: Antitoxin HigA

B: Endoribonuclease HigB

C: Antitoxin HigA

D: Endoribonuclease HigB

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

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

hetero molecules

defined by author
58.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Antitoxin HigA

F: Endoribonuclease HigB

G: Antitoxin HigA

H: Endoribonuclease HigB

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

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

hetero molecules

defined by author
58.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.150, 98.130, 147.190
Angle α, β, γ (deg.)	90.000, 109.490, 90.000
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	I-124- HOH

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein	Antitoxin HigA / Antidote protein / Host inhibition of growth protein A Mass: 11690.636 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A224
#2: Protein	Endoribonuclease HigB / Host inhibition of growth protein B / Killer protein / Toxin HigB / mRNA interferase HigB Mass: 10983.193 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higB / Production host: Escherichia coli (E. coli) References: UniProt: Q7A225, Hydrolases; Acting on ester bonds

#1: Protein

Antitoxin HigA / Antidote protein / Host inhibition of growth protein A

Mass: 11690.636 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Proteus vulgaris (bacteria) / Gene: higA / Production host:

Escherichia coli (E. coli) / References: UniProt: Q7A224

#2: Protein

Endoribonuclease HigB / Host inhibition of growth protein B / Killer protein / Toxin HigB / mRNA interferase HigB

Mass: 10983.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Proteus vulgaris (bacteria) / Gene: higB / Production host:

Escherichia coli (E. coli)
References: UniProt: Q7A225, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 4 molecules IKJL

#3: DNA chain	DNA (5'-D(GPTPAPTPTPAPCPAPCPAPCPCPAPTPGPTPAPAPTPAPC)-3') Mass: 6390.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Proteus vulgaris* (bacteria)
#4: DNA chain	DNA (5'-D(GPTPAPTPTPAPCPAPTPGPGPTPGPTPGPTPAPAPTPAPC)-3') Mass: 6492.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Proteus vulgaris* (bacteria)

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Non-polymers , 3 types, 338 molecules

#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.87 Å³/Da / Density % sol: 57.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Tris-HCl, KCl, MgCl2, 2-mercaptoethanol, NaCl, EDTA, CaCl2, PEG 3350 PH range: 7.5-8

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9792 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.4→67.3 Å / Num. obs: 98818 / % possible obs: 97.5 % / Redundancy: 2.777 % / B_iso Wilson estimate: 53.629 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.066 / R_rim(I) all: 0.081 / Χ²: 1.182 / Net I/σ(I): 9.13

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.4-2.5	2.056	0.465	1.76	11151	0.798	0.62	95
2.5-2.6	2.4	0.329	2.61	9227	0.899	0.418	93.5
2.6-3	2.96	0.197	4.88	27594	0.967	0.24	98.9
3-4	2.915	0.07	11.56	29282	0.993	0.085	98
4-5	2.901	0.051	17.33	10547	0.994	0.062	98.1
5-6	2.867	0.045	17.62	4633	0.995	0.055	98.5
6-8	2.875	0.041	17.96	3691	0.996	0.05	98.4
8-10	2.981	0.035	20.27	1323	0.997	0.042	97.6
10-20	2.769	0.03	20.24	1202	0.997	0.037	97.6
20-35	3.09	0.037	22.27	144	0.996	0.045	97.3
35-67.3	2.958	0.094	21.8	24	0.983	0.117	92.3

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	1.17.1	refinement
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4MCX

4mcx

Resolution: 2.4→67.3 Å / Cross valid method: FREE R-VALUE

	R_factor	Num. reflection	% reflection
R_free	0.2211	2537	-
R_work	0.1747	-	-
obs	-	95528	94.34 %

Displacement parameters

B_iso max: 169.53 Å² / B_iso mean: 57.3775 Å² / B_iso min: 27.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→67.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6095	1710	19	319	8143

LS refinement shell

Resolution: 2.4→2.486 Å

	R_factor	Num. reflection	% reflection
R_free	0.3414	-	-
R_work	0.2964	-	-
obs	-	4965	97.27 %

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	6.9679	-1.2957	1.8011	3.2027	-3.0234	3.46	-0.2592	0.4593	0.4551	-1.262	0.5963	-0.0496	-0.1995	-0.7735	-0.1633	0.6741	-0.0469	0.0628	0.5911	0.0251	0.4573	43.8249	84.8763	-27.397
2	8.2093	0.7427	-4.1664	8.2443	1.4174	9.9375	0.2427	-0.3315	1.0566	0.291	-0.3134	0.2727	-1.0599	-0.8066	0.0733	0.5492	-0.0691	-0.0573	0.4609	-0.0444	0.4806	39.9647	74.0163	-14.8398
3	2.9099	2.8934	3.8432	6.7904	1.3373	6.6559	0.525	-0.9657	-0.4652	0.6912	-0.4651	0.1059	1.0884	-0.9649	-0.2021	0.5798	-0.1342	-0.0038	0.4107	0.0013	0.3442	37.8116	62.0101	-11.5669
4	1.9256	-0.7598	1.4273	0.3557	-0.0087	2.5093	0.1584	0.1807	-0.0682	-0.0534	-0.0604	-0.1113	0.1794	0.0435	-0.0691	0.3978	-0.1193	0.0102	0.293	0.0035	0.2933	40.1143	64.6488	-21.7143
5	8.8851	4.2371	-6.2393	9.2309	-3.1056	4.4054	0.2769	0.682	0.4597	-0.1629	0.2941	0.0084	0.0701	-0.095	-0.6531	0.4168	-0.0516	-0.0107	0.4522	0.002	0.308	39.8303	74.1949	-29.9559
6	0.8009	-1.5205	-1.7736	2.9057	3.3965	4.0058	0.7774	-0.3772	1.4274	0.6147	0.3458	0.3664	-1.3478	1.4891	-0.7362	0.6114	-0.1052	0.0529	0.5851	0.0314	0.6847	52.2711	79.2424	-38.2395
7	0.8154	-0.7613	-0.1537	1.9647	-0.5749	0.907	-0.1943	0.0095	0.6689	-0.0912	-0.098	0.0103	-0.2944	-0.0689	0.2597	0.6147	-0.2831	-0.056	0.7219	0.0313	0.5423	44.7239	87.2724	-56.0199
8	8.702	1.2387	1.4337	4.3818	3.6938	7.4467	-0.2023	1.1392	0.3	-1.4212	0.303	0.2635	-0.9596	-0.3986	0.0815	0.6817	-0.0082	-0.0106	0.7264	0.0672	0.7356	31.957	92.1479	-26.8162
9	5.637	1.8262	-0.4021	6.3093	1.8063	4.1506	0.0877	-0.0023	0.5935	0.3155	-0.1849	0.1233	-0.0806	0.1813	0.0537	0.459	-0.0489	0.0224	0.4612	0.0112	0.5122	41.8556	93.9952	-20.9853
10	8.4116	4.2831	3.5187	9.1764	4.641	2.578	0.2874	-0.5122	-0.4646	0.5988	-0.1764	0.2308	0.2531	-0.2927	-0.1084	0.4471	-0.1123	0.0518	0.4055	0.052	0.4331	38.4419	83.8868	-18.5928
11	5.5739	-3.59	-0.2846	3.6438	0.1503	0.679	-0.1765	-0.2332	-0.0041	0.1935	0.0684	1.1967	0.1285	-0.4191	0.0837	0.5044	-0.1059	0.1109	0.4953	-0.0652	0.778	24.3881	80.76	-20.1592
12	0.7766	-1.4718	-0.464	8.1939	0.3259	0.2815	0.2343	-1.0475	-0.1467	0.4823	0.5043	1.1861	-0.9368	-0.2498	-0.4413	0.7074	-0.0566	0.2723	0.5218	-0.0473	0.587	27.7685	86.1802	-14.3617
13	4.5794	-3.7641	1.2439	5.9405	-3.8766	3.093	0.198	0.1368	0.3777	0.4777	-0.0296	1.2615	-1.1951	-0.6412	-0.6379	0.6371	-0.101	0.018	0.5212	-0.0381	0.8044	26.9184	89.6599	-19.6302
14	2.6443	-1.944	0.4924	3.3139	-2.1378	1.7672	2.1029	0.7951	-0.2975	0.0988	0.1997	0.6039	1.1711	-0.3828	-1.2713	0.7457	-0.1647	-0.2328	0.7952	0.1603	0.6551	25.9015	90.5559	-30.9652
15	7.9368	1.9645	2.1562	0.499	0.5662	0.6356	-0.6593	-0.2183	-0.0174	0.3438	0.1457	1.0642	-0.877	-0.4187	0.2337	0.6274	-0.0639	0.1812	0.5025	-0.1073	0.8068	29.4652	92.7697	-14.4251
16	9.5021	-0.9179	-0.6641	2.7879	0.8398	6.0341	0.2945	-0.5425	-0.0037	0.1635	-0.3705	0.356	-0.0925	-0.1417	0.1812	0.518	-0.0663	0.07	0.487	0.0385	0.4512	24.4934	65.6574	-41.9455
17	8.2637	-0.377	0.1543	7.6787	-6.4035	9.2484	-0.1037	-0.2821	0.6223	-0.3458	-0.0067	0.7656	-0.0018	-0.7074	-0.023	0.3905	-0.0927	-0.0427	0.5059	-0.0226	0.4999	35.3724	69.4566	-54.521
18	5.5299	3.3298	2.9432	3.2901	4.6091	7.7475	-0.1053	1.2222	-0.0891	-0.8237	0.6257	-0.8432	-0.6867	1.1553	-0.5558	0.5132	-0.16	0.0217	0.6304	-0.0118	0.4371	47.4249	71.5667	-57.8493
19	0.2211	-0.5743	-0.5337	1.0822	1.0056	2.8195	-0.1701	0.0437	-0.066	-0.0406	0.1773	0.08	-0.1555	0.4467	-0.0035	0.3088	-0.1228	0.0243	0.4005	-0.0053	0.3662	44.7848	69.33	-47.6579
20	8.5813	4.2358	-2.6037	9.304	-4.6272	7.9114	0.3092	0.1237	-0.0133	0.9237	0.0793	0.2692	-0.1154	0.3083	-0.3783	0.3243	-0.0409	0.03	0.3152	-0.0481	0.2821	35.0982	69.0442	-39.0516
21	1.9498	-1.3347	-0.8795	3.9985	0.6376	6.5082	0.0386	0.2008	0.0304	0.2192	-0.3703	0.3253	1.1164	-0.4474	0.3913	0.4696	-0.1742	0.0826	0.4569	0.008	0.5588	27.8922	60.9549	-20.2151
22	1.4471	0.1982	-1.9213	0.413	-1.2627	5.2961	0.1661	-0.2276	0.625	0.4548	-1.0907	0.3362	0.1868	0.2812	-0.0945	0.9162	-0.374	-0.0568	0.6226	-0.1146	0.8849	15.0604	68.4642	-9.8754
23	7.9047	1.0288	5.7279	7.8704	2.9997	5.0546	0.4083	-1.5207	0.1725	0.6672	-0.2265	0.1603	-0.016	-1.2888	-0.0495	0.5382	0.0032	0.0924	0.6134	0.0224	0.6999	17.2733	77.5328	-42.5548
24	4.5	-0.1722	0.7514	3.8693	1.5081	6.8805	0.0019	-0.0094	0.3299	0.3435	0.1303	0.2242	0.4835	-0.3028	-0.1141	0.4897	-0.0994	0.0168	0.48	0.0064	0.4757	15.4343	67.6044	-48.3701
25	6.9519	3.274	5.6877	7.0456	5.0114	5.7503	-0.0806	0.1699	0.0516	-0.594	0.0448	-0.5019	-0.5132	0.1133	-0.0422	0.4158	-0.1549	0.0558	0.4595	0.0178	0.4562	25.6176	71.0437	-50.8019
26	0.2769	-0.6483	-0.4744	5.0609	4.0336	3.2882	0.1476	-0.0142	1.1445	1.1392	-0.2161	-0.2312	-1.2638	0.9704	-0.0072	0.5832	-0.0887	-0.0318	0.4439	-0.0502	0.5727	30.8836	82.8846	-42.0706
27	4.5259	-5.9472	0.9947	8.092	-1.2526	0.9912	-0.0592	0.4877	0.8278	-0.7978	0.038	0.2672	-0.0654	0.1837	0.0837	0.4965	-0.049	-0.0999	0.4984	0.1881	0.8153	27.7702	86.0573	-52.6305
28	6.8968	-2.691	-4.4258	6.3063	0.8824	7.8114	0.1412	0.6453	1.4628	-0.0284	-0.0128	0.2305	-0.6993	-0.6866	-0.2199	0.3815	-0.1105	-0.0733	0.5996	0.0263	0.6956	21.0399	82.373	-49.6551
29	0.5303	1.4882	-0.9195	3.8336	-2.4283	1.6298	-0.5026	0.7832	1.7819	-0.4354	-0.4234	-0.5074	-0.8329	-0.7085	0.3656	0.5736	-0.0089	-0.107	0.7138	0.105	0.8664	16.6191	79.9824	-54.9265
30	3.5689	-0.6919	-1.3924	3.2526	-1.3667	5.3751	-0.0261	0.2386	-0.2114	0.0043	0.002	0.1813	0.9485	-0.0642	0.0537	0.6472	-0.0542	-0.067	0.5247	-0.0126	0.3812	49.1021	61.2273	-8.9244
31	2.6687	-0.0247	1.1635	3.3522	-2.817	2.8385	0.3431	-0.0989	-0.3519	-0.4232	0.2623	-0.1432	1.4341	0.6333	-0.5722	0.6613	0.0915	-0.0709	0.6284	-0.1034	0.4562	52.8208	56.0144	-33.2456
32	6.0762	0.0581	0.6756	7.7566	0.8041	2.2049	0.1528	0.1018	-1.0969	-1.7078	0.3512	-0.6982	-0.5543	1.3681	-0.4666	0.613	0.0441	0.05	0.8039	-0.193	0.4546	56.2381	55.36	-58.0929
33	5.7257	6.2592	1.415	6.907	0.6576	9.0938	0.9543	1.0518	-0.3227	0.665	-0.4942	0.7337	0.7941	0.182	-0.3809	0.8585	0.0266	0.01	1.0003	-0.2383	0.4792	48.453	54.4243	-68.1829
34	6.7294	0.1044	0.933	4.8978	-0.595	2.0198	0.0022	-0.3798	-0.2312	-0.2365	0.4259	-0.4116	0.9575	0.3914	-0.3653	0.5625	0.0596	0.0439	0.6186	-0.1787	0.4206	52.4864	57.0937	-52.2914
35	3.1097	0.4062	2.2295	5.1404	-1.1351	3.9106	0.2677	-0.1542	-0.2674	-0.0477	0.1483	-0.4003	1.2195	0.4904	-0.3789	0.6157	0.079	-0.0898	0.5575	-0.0581	0.3966	52.3944	56.6583	-18.2144
36	2.1502	0.58	1.7591	4.8014	-1.155	5.7024	0.551	-0.0773	0.1001	-0.3561	-0.1654	-0.3961	0.2961	0.4362	-0.2088	0.5633	-0.0701	0.0097	0.5583	-0.028	0.5124	73.6356	104.0852	-41.9294
37	5.2722	-1.0698	-2.3156	7.645	5.2842	4.2475	-0.1994	0.2294	-0.2851	-0.0518	0.1688	-0.8461	0.6617	0.8695	0.058	0.4309	-0.0554	0.0316	0.5283	0.0561	0.4617	62.719	100.3284	-54.5211
38	5.3268	1.8174	-1.0517	3.8441	-5.4739	8.2561	0.0903	0.918	0.0887	-0.7196	0.4699	0.8743	1.0902	-1.0271	-0.6309	0.4547	-0.1268	-0.0117	0.5621	-0.0168	0.405	50.744	98.2321	-57.8391
39	0.3627	0.0241	0.551	2.5738	-1.3717	1.931	-0.0896	-0.0653	0.0982	0.1235	0.2093	-0.064	0.0125	-0.3491	-0.1212	0.2963	-0.1159	0.0157	0.4382	0.0187	0.3412	53.3831	100.4666	-47.6548
40	8.8503	4.8744	2.5242	8.0435	5.8463	8.956	0.2806	0.2364	-0.0731	0.8748	0.1426	-0.3647	0.0722	0.1686	-0.4015	0.3667	-0.0857	0.0237	0.4228	0.0502	0.334	62.9315	100.2079	-39.4096
41	4.0851	-0.5255	2.2178	4.5911	-1.0604	5.1004	-0.0262	-0.038	0.1406	0.5456	-0.1627	-0.3955	-0.9839	0.2935	0.162	0.4906	-0.1901	0.013	0.3731	-0.0001	0.3981	70.0224	109.1034	-21.1086
42	0.0562	-0.0736	-0.0293	0.0132	0.0142	0.0117	-0.3178	0.4376	-0.6696	-0.0005	-0.1444	-1.1789	0.2997	0.0608	-0.0541	0.9747	-0.2384	-0.0009	0.7896	0.0366	1.0296	83.1736	101.312	-9.841
43	9.3315	2.861	-6.4404	4.8315	-3.1584	4.9514	0.7831	-1.4193	-0.5359	0.8343	-0.5495	-0.2939	-0.5233	0.7386	-0.0079	0.633	-0.069	-0.0558	0.6849	0.0016	0.6634	80.8989	92.2555	-42.58
44	5.1601	1.7595	-2.4685	4.6509	0.4388	4.3788	0.1571	0.2222	-0.2591	0.2515	0.0967	-0.3445	-0.3229	0.1198	-0.2213	0.3731	-0.0795	0.0158	0.4199	-0.0486	0.4489	82.7169	102.1728	-48.4
45	9.0881	4.6748	-7.7921	6.9165	-5.3779	7.7127	-0.3909	0.2525	-0.0305	-0.5776	0.1673	0.4349	0.6352	-0.6345	0.164	0.3933	-0.0825	-0.0372	0.4189	-0.0228	0.4625	72.5831	98.773	-50.7926
46	2.8576	-3.8046	-0.3069	7.0483	-0.078	2.6186	-0.0897	0.069	-0.8953	-0.1601	0.1803	-0.3254	0.1574	-0.241	-0.087	0.4559	-0.0809	0.052	0.4923	-0.0822	0.735	69.3937	84.7475	-49.2623
47	8.3477	-2.393	4.1135	8.7196	-2.8917	5.9535	0.237	0.4825	-1.2264	-0.0448	-0.1922	-0.4053	0.5926	0.856	-0.0911	0.4226	-0.0511	0.0953	0.5111	-0.0102	0.6608	77.1457	87.404	-49.6417
48	2.1979	2.1325	1.3151	3.688	0.9099	0.9133	0.753	0.3622	-1.4016	-0.4895	0.2356	-0.0638	0.1706	0.0859	-0.8208	0.4868	-0.1561	0.0859	0.6448	-0.1772	0.852	81.1739	90.0202	-54.869
49	2.8716	0.3971	-1.852	2.1246	1.3104	5.6093	-0.1394	0.0514	-0.5785	-0.1417	0.5324	0.298	0.3559	0.4068	-0.3103	0.5787	-0.0361	-0.0821	0.5757	0.0004	0.4631	54.3404	84.9322	-27.4274
50	6.6591	-0.0311	2.565	7.5327	-1.2681	3.7213	0.358	-0.2704	-0.9574	0.6036	-0.101	-0.2338	0.956	0.1972	-0.1985	0.557	-0.1067	0.0513	0.4699	0.0395	0.4052	58.1836	95.7073	-14.8815
51	9.7211	2.0086	-3.9491	6.742	-0.3018	4.2457	0.3849	-0.7398	0.7529	0.8453	0.3062	0.0467	-1.0103	0.4176	-0.6816	0.585	-0.1438	0.0081	0.4148	-0.0236	0.3219	60.3025	107.8182	-11.5687
52	0.7498	-0.104	-1.0635	0.4674	-0.0684	2.2283	0.1505	-0.0413	-0.0428	0.1056	-0.1701	0.1468	-0.2809	0.0325	0.0139	0.4313	-0.1307	0.0244	0.323	-0.0257	0.3611	58.0469	105.1297	-21.7073
53	5.1107	6.0827	3.5383	8.7371	1.8962	4.977	-0.0784	0.9691	-0.1692	0.0471	0.3799	-0.148	-0.0112	-0.0416	-0.2377	0.4652	-0.0618	0.0448	0.4293	0.0164	0.3118	58.3138	95.5695	-29.9572
54	4.0676	-1.524	-0.7936	4.0373	2.2757	4.7394	-0.0212	0.3965	-0.293	-0.0855	0.0925	-0.0595	0.0887	-0.833	0.0218	0.4603	-0.2207	0.0057	0.4545	-0.0018	0.3851	49.3772	88.5398	-48.2361
55	0.4211	-0.1051	1.0747	5.178	3.709	6.4928	-0.5624	0.3784	-0.955	0.0195	-0.1484	-0.44	-0.6668	-0.2486	-0.229	0.7643	-0.3989	0.093	0.8824	0.1487	0.8773	57.1869	75.3397	-59.4097
56	8.4122	1.9178	-3.2792	5.5303	-0.4214	7.4477	-0.6104	0.795	-0.6259	-1.5686	0.6076	-0.3656	0.5919	0.3774	0.1602	0.5568	-0.0488	-0.0071	0.6553	-0.0693	0.5816	66.2455	77.5824	-26.7963
57	3.3861	1.6651	-0.9828	5.6794	-1.5327	2.0621	0.1007	-0.2914	0.0461	0.3335	-0.0738	-0.1362	0.209	-0.0875	0.0083	0.4111	-0.108	-0.0129	0.3424	-0.0294	0.3876	58.1164	81.1313	-19.7176
58	4.247	-0.8019	-2.7822	2.9088	0.3785	1.8753	-0.0296	0.977	-0.7511	-0.5942	-0.2265	-1.7053	-0.6731	0.8551	0.2797	0.5145	-0.1118	0.0737	0.5952	0.0247	0.5917	71.5301	91.2358	-27.2999
59	7.2748	-5.8274	0.168	4.7564	-0.4306	3.1844	0.2278	-1.2493	-0.5818	0.0976	0.0399	-0.8466	-0.3267	-0.0696	-0.0688	0.5648	-0.0673	-0.1447	0.4326	0.1311	0.9131	74.7103	88.1246	-16.8189
60	5.4127	-3.3126	0.1066	6.4983	4.8294	6.7101	0.1053	-0.0023	-0.2575	0.6099	0.2331	-1.3	0.7316	0.4066	-0.3659	0.5023	-0.1139	-0.0415	0.3809	0.0198	0.6736	71.0897	81.3674	-19.7584
61	3.6866	0.5296	-0.4829	0.1151	-0.0414	0.1148	-0.2401	-0.1298	-0.2037	0.1502	0.4956	-1.1731	0.4514	0.6985	-0.1905	0.6772	-0.0945	-0.1135	0.4439	0.062	0.7378	68.6718	76.9953	-14.3961
62	3.223	0.1752	-0.0042	4.1923	0.0845	5.0586	0.2259	0.0747	0.2513	-0.0786	0.1003	0.3277	-0.6926	-0.6568	-0.2346	0.5956	0.0682	0.156	0.4933	-0.0059	0.3996	45.8135	112.8089	-16.9658
63	7.5575	2.7417	3.8332	7.1954	6.3943	6.9211	0.1665	-0.1654	-0.1066	-0.4505	0.313	-0.3251	-1.2247	-0.8593	-0.4299	0.5936	0.0018	0.0775	0.5209	0.0915	0.3496	48.0418	110.5614	-41.6066
64	3.1175	-0.8137	-0.9901	3.4768	1.074	4.5478	0.3112	0.3609	0.5558	-0.4502	0.2127	0.5646	-0.558	-1.3516	-0.5369	0.7007	0.0869	0.0013	0.8551	0.1949	0.4872	43.1601	114.5806	-59.6849
65	0.7584	0.2154	1.4844	0.3793	-0.0148	5.7751	0.1025	-0.1239	0.1056	0.1258	0.2225	0.1527	-0.536	-0.9857	-0.3058	0.5812	0.0382	0.0436	0.6377	0.111	0.4814	46.4519	111.9597	-43.9087
66	4.2494	1.598	-3.6402	2.7294	-3.0013	9.218	0.4141	-0.5619	0.6215	0.1662	0.0786	0.5278	-0.6242	-0.0794	-0.4713	0.8218	0.1509	0.2519	0.6173	0.0075	0.4839	43.9439	115.3878	-9.6884

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 8 )	A	1 - 8
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 9 through 20 )	A	9 - 20
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 21 through 31 )	A	21 - 31
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 32 through 63 )	A	32 - 63
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 64 through 78 )	A	64 - 78
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 79 through 83 )	A	79 - 83
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 84 through 101 )	A	84 - 101
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 7 )	B	0 - 7
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 8 through 23 )	B	8 - 23
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 24 through 39 )	B	24 - 39
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 40 through 62 )	B	40 - 62
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 63 through 71 )	B	63 - 71
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 72 through 79 )	B	72 - 79
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 80 through 84 )	B	80 - 84
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 85 through 91 )	B	85 - 91
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 8 )	C	1 - 8
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 9 through 20 )	C	9 - 20
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 21 through 31 )	C	21 - 31
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 32 through 63 )	C	32 - 63
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 64 through 79 )	C	64 - 79
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 80 through 94 )	C	80 - 94
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 95 through 102 )	C	95 - 102
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 0 through 7 )	D	0 - 7
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 8 through 23 )	D	8 - 23
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 24 through 39 )	D	24 - 39
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 40 through 46 )	D	40 - 46
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 47 through 62 )	D	47 - 62
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 63 through 84 )	D	63 - 84
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 85 through 91 )	D	85 - 91
30	X-RAY DIFFRACTION	30	chain 'I' and (resid 1 through 5 )	I	1 - 5
31	X-RAY DIFFRACTION	31	chain 'I' and (resid 6 through 15 )	I	6 - 15
32	X-RAY DIFFRACTION	32	chain 'I' and (resid 16 through 20 )	I	16 - 20
33	X-RAY DIFFRACTION	33	chain 'I' and (resid 21 through 21 )	I	21
34	X-RAY DIFFRACTION	34	chain 'J' and (resid 1 through 10 )	J	1 - 10
35	X-RAY DIFFRACTION	35	chain 'J' and (resid 11 through 21 )	J	11 - 21
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 1 through 8 )	E	1 - 8
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 9 through 20 )	E	9 - 20
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 21 through 31 )	E	21 - 31
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 32 through 63 )	E	32 - 63
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 64 through 78 )	E	64 - 78
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 79 through 94 )	E	79 - 94
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 95 through 102 )	E	95 - 102
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 0 through 7 )	F	0 - 7
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 8 through 23 )	F	8 - 23
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 24 through 39 )	F	24 - 39
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 40 through 62 )	F	40 - 62
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 63 through 84 )	F	63 - 84
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 85 through 91 )	F	85 - 91
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 1 through 8 )	G	1 - 8
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 9 through 20 )	G	9 - 20
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 21 through 31 )	G	21 - 31
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 32 through 63 )	G	32 - 63
53	X-RAY DIFFRACTION	53	chain 'G' and (resid 64 through 78 )	G	64 - 78
54	X-RAY DIFFRACTION	54	chain 'G' and (resid 79 through 94 )	G	79 - 94
55	X-RAY DIFFRACTION	55	chain 'G' and (resid 95 through 102 )	G	95 - 102
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 0 through 7 )	H	0 - 7
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 8 through 39 )	H	8 - 39
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 40 through 46 )	H	40 - 46
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 47 through 62 )	H	47 - 62
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 63 through 84 )	H	63 - 84
61	X-RAY DIFFRACTION	61	chain 'H' and (resid 85 through 91 )	H	85 - 91
62	X-RAY DIFFRACTION	62	chain 'K' and (resid 1 through 10 )	K	1 - 10
63	X-RAY DIFFRACTION	63	chain 'K' and (resid 11 through 15 )	K	11 - 15
64	X-RAY DIFFRACTION	64	chain 'K' and (resid 16 through 21 )	K	16 - 21
65	X-RAY DIFFRACTION	65	chain 'L' and (resid 1 through 15 )	L	1 - 15
66	X-RAY DIFFRACTION	66	chain 'L' and (resid 16 through 21 )	L	16 - 21

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News

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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

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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.

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Protein , 2 types, 8 molecules ACEGBDFH

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DNA chain , 2 types, 4 molecules IKJL

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Protein , 2 types, 8 molecules ACEGBDFH

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