PDB-8cxw: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA...

ID or keywords:

Entry

Database: PDB / ID: 8cxw

Title

CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor piclidenoson (Compound 4)

Components

DNA Strand 1DNA
DNA Strand 2DNA
Site-specific DNA-methyltransferase (adenine-specific)DNA methyltransferase

Keywords

DNA BINDING PROTEIN/DNA /

DNA Adenine Methylation /

PROTEIN-DNA COMPLEX /

TRANSFERASE /

DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

Function / homology

Function and homology information

N-methyltransferase activity /

site-specific DNA-methyltransferase (adenine-specific) /

site-specific DNA-methyltransferase (adenine-specific) activity /

Biological species

Clostridioides difficile 630 (bacteria)

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.78 Å

Authors

Horton, J.R. / Zhou, J. / Cheng, X.

Funding support

United States, 1items

Citation

Journal: J.Med.Chem. / Year: 2023
Title: Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / ...

History

Deposition	May 22, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2023	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2	Jan 25, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8cxw.cif.gz	934.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8cxw.ent.gz	638.7 KB	Display	PDB format
PDBx/mmJSON format	8cxw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cx/8cxw ftp://data.pdbj.org/pub/pdb/validation_reports/cx/8cxw	HTTPS FTP

-
Related structure data

Related structure data	8cxsC 8cxtC 8cxuC 8cxvC 8cxxC 8cxyC 8cxzC 8cy0C 8cy1C 8cy2C 8cy3C 8cy4C 8cy5C 7lnjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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) #91 - Jul 2007 Thymine Dimers similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #253 - Jan 2021 Expressome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #135 - Mar 2011 Integrase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #23 - Nov 2001 DNA similarity (1) #190 - Oct 2015 Two-component Systems 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)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Site-specific DNA-methyltransferase (adenine-specific)

B: Site-specific DNA-methyltransferase (adenine-specific)

C: Site-specific DNA-methyltransferase (adenine-specific)

D: DNA Strand 1

E: DNA Strand 2

F: DNA Strand 1

G: DNA Strand 2

H: DNA Strand 1

I: DNA Strand 2

hetero molecules

234 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Site-specific DNA-methyltransferase (adenine-specific)

D: DNA Strand 1

E: DNA Strand 2

hetero molecules

defined by author&software
Evidence: isothermal titration calorimetry
78.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Site-specific DNA-methyltransferase (adenine-specific)

F: DNA Strand 1

G: DNA Strand 2

hetero molecules

defined by author&software
78.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Site-specific DNA-methyltransferase (adenine-specific)

H: DNA Strand 1

I: DNA Strand 2

hetero molecules

defined by author&software
78 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.326, 161.634, 229.602
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

-
Protein , 1 types, 3 molecules ABC

#1: Protein	Site-specific DNA-methyltransferase (adenine-specific) / DNA methyltransferase / CamA methyltransferase Mass: 68887.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile 630 (bacteria) Strain: 630 / Gene: CD630_27580 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: Q183J3, site-specific DNA-methyltransferase (adenine-specific)

#1: Protein

Site-specific DNA-methyltransferase (adenine-specific) /

DNA methyltransferase / CamA methyltransferase

Mass: 68887.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridioides difficile 630 (bacteria)
Strain: 630 / Gene: CD630_27580 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q183J3,

site-specific DNA-methyltransferase (adenine-specific)

-
DNA chain , 2 types, 6 molecules DFHEGI

#2: DNA chain	DNA Strand 1 / DNA Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain	DNA Strand 2 / DNA Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)

-
Non-polymers , 4 types, 379 molecules

#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-Q8L / Piclidenoson Mass: 510.286 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₈H₁₉IN₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.42 Å³/Da / Density % sol: 64.04 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 21~24% (w/v) polyethylene glycol 3350, 0.1 M Tris-HCl pH 7.0~7.5, 0.28 M potassium citrate PH range: 7.0-7.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.78→46.8 Å / Num. obs: 76354 / % possible obs: 99.6 % / Redundancy: 5.1 % / B_iso Wilson estimate: 48.58 Å² / R_merge(I) obs: 0.224 / R_pim(I) all: 0.11 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.78→2.89 Å / Redundancy: 4.5 % / R_merge(I) obs: 1.51 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7506 / CC_1/2: 0.394 / CC star: 0.752 / R_pim(I) all: 0.789 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
SERGUI		data collection
PHENIX	1.20.1_4487	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 7LNJ

7lnj

Resolution: 2.78→46.8 Å / SU ML: 0.3297 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.6276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2274	1998	2.62 %
R_work	0.1845	74170	-
obs	0.1857	76168	99.28 %

Solvent computation

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

Displacement parameters

B_iso mean: 56.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.78→46.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13359	1704	114	364	15541

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	15675
X-RAY DIFFRACTION	f_angle_d	0.4746	21491
X-RAY DIFFRACTION	f_chiral_restr	0.04	2354
X-RAY DIFFRACTION	f_plane_restr	0.0028	2460
X-RAY DIFFRACTION	f_dihedral_angle_d	16.7395	5985

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 (%)
2.78-2.85	0.3263	135	0.3015	5032	X-RAY DIFFRACTION	96.22
2.85-2.93	0.3526	143	0.2811	5266	X-RAY DIFFRACTION	99.54
2.93-3.02	0.3416	142	0.2672	5289	X-RAY DIFFRACTION	99.71
3.02-3.11	0.2747	141	0.2506	5244	X-RAY DIFFRACTION	99.67
3.11-3.22	0.334	142	0.2541	5239	X-RAY DIFFRACTION	99.67
3.22-3.35	0.2628	141	0.2055	5261	X-RAY DIFFRACTION	99.5
3.35-3.51	0.2276	142	0.1865	5268	X-RAY DIFFRACTION	99.39
3.51-3.69	0.2449	143	0.1803	5306	X-RAY DIFFRACTION	99.54
3.69-3.92	0.2422	141	0.177	5242	X-RAY DIFFRACTION	99.3
3.92-4.23	0.1974	143	0.1498	5288	X-RAY DIFFRACTION	99.09
4.23-4.65	0.185	144	0.1344	5342	X-RAY DIFFRACTION	99.84
4.65-5.32	0.1645	144	0.1412	5367	X-RAY DIFFRACTION	99.6
5.32-6.7	0.1767	145	0.1703	5400	X-RAY DIFFRACTION	99.41
6.7-46.8	0.1907	152	0.1718	5626	X-RAY DIFFRACTION	99.43

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	2.6484115923	-0.317464271046	-1.04171444203	4.03894256371	1.12339191625	2.67279207486	-0.0405075956123	0.160802590223	-0.0223134932678	0.520450183422	-0.0265698317639	0.19499672264	-0.0190838755186	-0.244735462563	0.129059678556	0.478923221514	0.0651799190274	0.0757713311563	0.317529645527	-0.0189205215491	0.325275462264	-32.0837058876	1.2208766384	35.9526657909
2	0.831436352199	-0.88157264876	-0.595138365418	2.30156243809	1.51443461572	3.79888954081	0.102937642441	0.0428899771953	0.235908902921	-0.135307858405	-0.0610141367639	-0.0645104353586	-0.786847726701	-0.154669531338	-0.0656163645886	0.464080399837	-0.0271150174361	0.0661020290947	0.343848939409	-0.0376413963572	0.337921540731	-26.2532363278	1.95842016945	21.7110873868
3	3.26143825254	2.34804536221	-0.228246515238	3.7698634254	2.59633934972	4.412623174	0.279285604245	-0.256136763433	0.0410785710086	0.501875156276	-0.335041600111	-0.083309487361	0.26444516667	-0.1457643001	-0.13938808746	0.397183589621	0.0271299427461	0.021869284953	0.346950154695	-0.0336110831749	0.314626641496	-24.5363919854	-12.3446777067	24.5502305465
4	0.223180441688	-0.577629084238	-0.346746132245	1.56339421966	0.826988418371	3.96390252624	-0.130777664602	-0.020737764047	0.0785923076069	0.343928536531	0.0416967895829	-0.0339563021248	0.125090249867	0.129923297286	0.0896422590737	0.252187928821	-0.0522960050512	0.0318952302305	0.344740529747	-0.00686624392694	0.304330020763	-17.8883585971	-23.8615074932	18.7754393631
5	2.4638460003	-0.548454192636	1.30185471861	3.54878068417	0.0718745924646	1.40580162478	0.0326719319912	0.709467346039	-0.0937021128146	-0.99188912785	0.0725397432001	0.471636654011	-0.0594553259978	-0.0667728833571	-0.126501594382	0.437631905866	-0.0154939616923	-0.0416600772472	0.623674035789	-0.0261563772775	0.303642050222	-27.552879475	-27.2523675087	-16.5827205817
6	1.26013605261	0.0964525889662	0.469823567943	2.53099877148	-1.24065810821	2.34787976289	-0.0246687973134	0.0675484081241	-0.127870201656	-0.196597511264	-0.0769124601434	-0.194107488565	0.180041190441	0.259308368965	0.0703298759776	0.184568415318	-0.000847244465256	0.0924219257097	0.361426411156	-0.0295344572381	0.275118423326	-14.4360495831	-35.5431415278	3.58098285446
7	2.09738389366	-0.124097831656	1.42898324032	1.30142622735	-0.422884754891	4.67723362979	-0.0901514325986	0.0809815847006	0.134125449414	-0.0487239672374	-0.130752106519	0.011544696663	-0.430706752114	0.0177658038588	0.226845522332	0.366061666313	0.0669955733286	0.0595612039254	0.308189634024	0.103718905333	0.344660106531	-14.119470154	14.1302636511	-57.0795940759
8	6.1601217996	-0.0126444337691	0.914209526396	1.73121410436	1.19473472763	1.05246936837	-0.264788132066	0.300761598007	0.453685783672	-0.202514601011	0.255959771547	-0.135205360649	-1.05476140719	-0.827676057206	-0.0252129565895	0.70483218288	0.181511268606	0.0457549207162	0.416114651832	0.0878364062807	0.398920675079	-19.9278085529	17.6741025242	-47.4924839002
9	1.32166713209	-0.818088761289	0.498704515648	1.47657304114	-0.636393063615	1.50607222916	0.176260673416	0.0652638762387	0.0197337080627	-0.124162585853	-0.0476218375518	-0.00727053081493	0.0486490595671	0.0131012262702	-0.125375702574	0.210312977726	-0.00072529656269	0.041188734629	0.265093114397	0.041282172168	0.262369693737	2.81853697462	-13.3398041991	-29.2111274797
10	2.55452939153	-0.0611284646789	0.693844904342	2.72265560374	0.736329294483	2.38225032396	-0.119871502082	-0.851203123606	0.200598990536	1.24325356429	0.132034963311	-0.150352218071	0.138424520804	-0.0772195272859	-0.150543941273	1.2285082001	0.0710567299529	-0.0344838670342	0.68364954248	-0.0801951508286	0.591114274087	23.3164952052	53.1365349825	-7.54346340113
11	1.86186626337	-0.537093615221	-0.182305303447	2.95719320102	1.75277556035	2.51261190787	-0.224165843282	-0.32629645754	-0.172168726097	0.94180350852	-0.0557212366762	0.279019215614	0.300408329722	-0.0498557082234	0.280358639687	0.707591988442	0.065111333529	0.113972346839	0.372467141855	0.0544509597238	0.521451215073	19.5494746943	37.9765250862	-22.2114862333
12	0.784587774142	-0.305527406786	1.68770783347	5.25874235473	-0.242078966453	4.61986870266	-0.0381175786739	-0.278358662957	0.747091831364	-0.28960020245	-0.0415149481922	0.370700055869	-0.307390045712	-0.257700184566	-0.0054410825217	0.652541010044	0.191548567846	0.131559296713	0.414498373374	-0.0324132102472	0.79151202374	15.9860447464	53.0984908485	-29.011780412
13	2.44330648928	0.357113756022	1.00350867559	0.279261851372	-0.147362071234	4.31150241851	-0.0416028355945	0.0250781318172	0.0136961220931	0.155093545008	0.0717700907082	0.585379560081	-0.709932726061	-0.558194582603	-0.0341875582082	0.634284500177	0.262111521606	0.0910511442481	0.551576805463	-0.0371876752883	0.688069814204	7.76621612931	49.7680945695	-38.3142624223
14	3.9319650287	-2.83989134887	1.19160897797	3.2724697001	-0.295567227561	1.68055891063	0.0614732386204	0.268256306141	0.0296656548003	-0.359473697836	-0.121085172288	-0.187638917816	0.10639236171	0.348160605988	0.0886835945169	0.375448835026	0.0243243355613	0.0909768717229	0.326225217704	0.0465827189907	0.420174195808	31.6019307524	25.9227888108	-56.4667118451
15	5.1706965864	1.25101177656	-2.06328046579	1.22587649502	-2.21442930866	4.45112753733	-0.253713386823	-0.2297453536	-0.879215540332	-0.0134516952734	0.0178296292969	-0.0382390893944	0.942384453585	0.852105618664	0.344760409331	0.582583457361	0.198741814516	0.0350342569163	0.37499542901	0.0970261536162	0.701618690493	42.9703966212	13.4710251716	-46.7226451016
16	2.07238602507	-1.5052266903	0.408182480262	2.37646163781	-0.648058101863	1.54680267212	0.136690784009	0.0268634330575	-0.173898676953	-0.435974603369	-0.0785681545499	0.307783757203	0.0643405087234	-0.063702100425	-0.070136958976	0.381490340962	0.000397798677316	0.0624290496258	0.308456506648	0.0402314195205	0.522423630497	19.2577775684	30.9680605123	-53.8759088489
17	4.93832004695	-4.0828890803	-0.869774306408	5.04327488139	1.3746169811	3.60486717119	0.405338824077	0.395735889532	0.235296447571	-0.614007910992	-0.152674154695	0.265838110059	-0.582610791213	-0.122763433253	-0.307467649689	0.807566212147	0.128566387855	-0.110360359878	0.42190186018	0.104682168662	0.482540653872	13.670023389	44.307832736	-67.729930041
18	1.78838150464	-0.231372184987	1.07107945193	2.65521955621	-0.332984018169	0.900988620012	-0.20514809642	0.109165088447	-0.439988412216	0.0132838102142	-0.0841656824192	0.687970435051	0.248521145945	-0.977152046551	0.200991022366	0.26642371958	-0.138334906718	0.0189952250654	0.614355701938	-0.0783227475125	0.484249161111	-28.4671399305	-19.2845124741	2.24083731656
19	0.444626834886	-0.284909953427	0.915981966486	2.64579582899	-0.506713407757	1.62898837439	0.0473224545498	-0.605706634678	0.0601044810792	0.38627017061	-0.209102723296	0.922409060514	-0.13901229235	-0.930802431909	-0.0684498871042	0.302865982406	-0.0601741935434	0.205870527289	0.80603765306	-0.0562578910697	0.590998420614	-32.4587242643	-20.4226265537	4.3647495524
20	2.31716996876	-0.20984898778	-1.6240883788	1.78177382035	-0.67788750735	1.40759573324	0.40006928866	-0.178780536266	0.334770990133	0.0342921649156	-0.148881890641	-0.270377348997	-0.553983968384	0.74653042443	-0.171717251757	0.378017094705	-0.124114909374	0.0620209097096	0.530688874647	0.034118579371	0.326926688997	5.34894327151	-2.49455577386	-25.3821513697
21	0.540774085923	-0.653244002576	0.376400229019	0.692577751495	-0.699844426542	1.80411466728	-0.0311102271642	0.0201198620237	0.152082344223	-0.30009382457	-0.116936715325	-0.485403979335	-0.160077751513	0.366636514165	0.21444844987	0.416750019162	-0.0464112493946	0.175104827311	0.301187039933	0.045200235333	0.475605540041	8.33273188097	0.0367761141161	-28.3084144306
22	1.58279169438	-0.50760005332	1.34481506265	1.72146445063	1.8721238585	4.00836599229	-0.0866480748227	0.053483400341	0.110214539464	-0.0587606422842	-0.194651817568	-0.975994907984	-0.174901293304	0.594532485443	0.257162735724	0.535109809013	0.0197612013012	0.164821416981	0.461393064907	0.237897306296	0.853112753511	31.5638204982	33.0207925284	-41.5355282227
23	2.11743953176	-2.18538661896	-1.37472704427	2.27857149796	0.655568529999	5.12982219299	-0.10567949721	-0.759228862056	0.70485872303	-0.260897201665	-0.36908500296	-0.73202876035	-0.622717298544	1.0079422969	0.413119061128	0.405755981411	-0.0776785760599	-0.112362039065	0.496538001314	0.0846442999847	0.73777977129	34.7602421278	36.8913135817	-41.15475189

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 30 through 90 )	A	A	30 - 90	1 - 61
2	2	chain 'A' and (resid 91 through 246 )	A	A	91 - 246	62 - 212
3	3	chain 'A' and (resid 247 through 273 )	A	A	247 - 273	213 - 239
4	4	chain 'A' and (resid 274 through 359 )	A	A	274 - 359	240 - 325
5	5	chain 'A' and (resid 360 through 428 )	A	A	360 - 428	326 - 394
6	6	chain 'A' and (resid 429 through 577 )	A	A	429 - 577	395 - 543
7	7	chain 'B' and (resid 29 through 130 )	B	B	29 - 130	1 - 102
8	8	chain 'B' and (resid 131 through 160 )	B	B	131 - 160	103 - 132
9	9	chain 'B' and (resid 161 through 577 )	B	B	161 - 577	133 - 549
10	10	chain 'C' and (resid 30 through 129 )	C	C	30 - 129	1 - 100
11	11	chain 'C' and (resid 130 through 259 )	C	C	130 - 259	101 - 220
12	12	chain 'C' and (resid 260 through 292 )	C	C	260 - 292	221 - 253
13	13	chain 'C' and (resid 293 through 333 )	C	C	293 - 333	254 - 294
14	14	chain 'C' and (resid 334 through 399 )	C	C	334 - 399	295 - 360
15	15	chain 'C' and (resid 400 through 428 )	C	C	400 - 428	361 - 389
16	16	chain 'C' and (resid 429 through 535 )	C	C	429 - 535	390 - 496
17	17	chain 'C' and (resid 536 through 577 )	C	C	536 - 577	497 - 538
18	18	chain 'D' and (resid 1 through 14 )	D	D	1 - 14
19	19	chain 'E' and (resid 1 through 14 )	E	E	1 - 14
20	20	chain 'F' and (resid 1 through 14 )	F	F	1 - 14
21	21	chain 'G' and (resid 1 through 14 )	G	G	1 - 14
22	22	chain 'H' and (resid 1 through 14 )	H	H	1 - 14
23	23	chain 'I' and (resid 1 through 14 )	I	I	1 - 14

-
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

-
Protein , 1 types, 3 molecules ABC

-
DNA chain , 2 types, 6 molecules DFHEGI

-
Non-polymers , 4 types, 379 molecules

-
Details

-
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

-Protein , 1 types, 3 molecules ABC

-DNA chain , 2 types, 6 molecules DFHEGI

-Non-polymers , 4 types, 379 molecules

-Details

-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

-
Protein , 1 types, 3 molecules ABC

-
DNA chain , 2 types, 6 molecules DFHEGI

-
Non-polymers , 4 types, 379 molecules

-
Details

-
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