PDB-7lni: SeMet CamA Adenine Methyltransferase Complexed to Cognate Substra...

ID or keywords:

Entry

Database: PDB / ID: 7lni

Title

SeMet CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA

Components

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

Keywords

TRANSFERASE/DNA /

DNA Adenine Methylation /

PROTEIN-DNA COMPLEX /

TRANSFERASE / TRANSFERASE-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 (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.68 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix.
Authors: Zhou, J. / Horton, J.R. / Blumenthal, R.M. / Zhang, X. / Cheng, X.

History

Deposition	Feb 7, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jul 14, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7lni.cif.gz	921.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7lni.ent.gz	649.7 KB	Display	PDB format
PDBx/mmJSON format	7lni.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ln/7lni ftp://data.pdbj.org/pub/pdb/validation_reports/ln/7lni	HTTPS FTP

-
Related structure data

Related structure data	7lnjC 7lt5C C: citing same article (ref.)
Similar structure data	7lnj-2 7lni-2 7lnj-1 7lt5-1 3m4y-d 2oox-3 3i4l-d 4zg6-1 3dos-1 5x09-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7lnjC

7lt5C

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) #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)

E: DNA Strand 2

D: DNA Strand 1

F: DNA Strand 1

G: DNA Strand 2

H: DNA Strand 1

I: DNA Strand 2

hetero molecules

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

1

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

E: DNA Strand 2

D: DNA Strand 1

defined by author&software
Evidence: isothermal titration calorimetry
77.7 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
77.9 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
77.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.071, 160.985, 231.318
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

#1: Protein	Site-specific DNA-methyltransferase (adenine-specific) / DNA methyltransferase / CamA methyltransferase Mass: 69168.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (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)
#2: DNA chain	DNA Strand 2 / DNA Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain	DNA Strand 1 / DNA Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.6 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Tris-HCl pH 7.0, 24.5% PEG 3350, 0.28 M Potassium citrate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97795 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97795 Å / Relative weight: 1
Reflection	Resolution: 2.68→40.76 Å / Num. obs: 164334 / % possible obs: 99.9 % / Redundancy: 32.9 % / B_iso Wilson estimate: 49.93 Å² / R_merge(I) obs: 0.308 / R_pim(I) all: 0.053 / Net I/σ(I): 16.1
Reflection shell	Resolution: 2.68→2.79 Å / Redundancy: 23.8 % / R_merge(I) obs: 2.602 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 16826 / CC_1/2: 0.671 / R_pim(I) all: 0.513 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
SERGUI		data collection
PHENIX	1.19_4092	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.68→40.76 Å / SU ML: 0.3988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2228	3813	2.32 %
R_work	0.2028	160383	-
obs	0.2033	164196	99.19 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.71 Å²

Refinement step

Cycle: LAST / Resolution: 2.68→40.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13363	1704	12	266	15345

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15563
X-RAY DIFFRACTION	f_angle_d	0.423	21333
X-RAY DIFFRACTION	f_chiral_restr	0.0386	2348
X-RAY DIFFRACTION	f_plane_restr	0.0028	2382
X-RAY DIFFRACTION	f_dihedral_angle_d	16.3697	5888

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 (%)
2.68-2.72	0.5049	119	0.4222	4881	X-RAY DIFFRACTION	81.12
2.72-2.75	0.3586	136	0.3692	5934	X-RAY DIFFRACTION	99.56
2.75-2.79	0.3417	141	0.3436	6010	X-RAY DIFFRACTION	99.58
2.79-2.83	0.4064	140	0.3239	5973	X-RAY DIFFRACTION	99.67
2.83-2.87	0.298	137	0.2934	5936	X-RAY DIFFRACTION	99.84
2.87-2.92	0.3298	141	0.2868	6031	X-RAY DIFFRACTION	99.82
2.92-2.97	0.274	142	0.2709	5937	X-RAY DIFFRACTION	99.93
2.97-3.02	0.2916	143	0.2695	6018	X-RAY DIFFRACTION	99.97
3.02-3.07	0.2806	140	0.2677	5942	X-RAY DIFFRACTION	99.97
3.07-3.13	0.266	141	0.2651	6018	X-RAY DIFFRACTION	99.97
3.13-3.2	0.3009	140	0.2698	5971	X-RAY DIFFRACTION	100
3.2-3.26	0.2859	142	0.2437	6003	X-RAY DIFFRACTION	99.98
3.26-3.34	0.2732	143	0.2109	5967	X-RAY DIFFRACTION	100
3.34-3.42	0.2256	142	0.2019	6018	X-RAY DIFFRACTION	99.98
3.42-3.52	0.2357	145	0.1874	5961	X-RAY DIFFRACTION	100
3.52-3.62	0.1875	143	0.1868	5970	X-RAY DIFFRACTION	99.98
3.62-3.74	0.2114	145	0.1886	6010	X-RAY DIFFRACTION	99.89
3.74-3.87	0.2209	142	0.187	5949	X-RAY DIFFRACTION	99.97
3.87-4.02	0.1731	147	0.1708	6025	X-RAY DIFFRACTION	99.92
4.02-4.21	0.176	143	0.1577	5961	X-RAY DIFFRACTION	99.92
4.21-4.43	0.1864	147	0.158	5963	X-RAY DIFFRACTION	99.93
4.43-4.71	0.1951	141	0.1485	5982	X-RAY DIFFRACTION	99.98
4.71-5.07	0.1779	148	0.156	6014	X-RAY DIFFRACTION	99.98
5.07-5.58	0.1811	141	0.1672	5961	X-RAY DIFFRACTION	99.97
5.58-6.38	0.2264	139	0.1864	6026	X-RAY DIFFRACTION	99.97
6.38-8.03	0.1746	142	0.1934	5947	X-RAY DIFFRACTION	99.89
8.03-40.76	0.1618	143	0.1784	5975	X-RAY DIFFRACTION	99.63

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	2.1288637902	0.739717344388	0.584822980952	5.54790236555	4.79939478739	9.32551959705	-0.0577773055536	0.112287492451	0.125872565191	0.168664343074	-0.103402502193	0.259615806145	-0.540827919866	-0.285440821585	0.177805256334	0.407249857444	0.0347129778454	0.0778919545445	0.347750803901	-0.023816669185	0.392208470893	-33.9870200601	4.79323819163	34.4320900224
2	2.07536244148	-0.976064083678	-1.43477546076	3.63900381326	1.75941339716	3.95823080325	0.150639927112	0.0279966426472	0.376388483241	-0.161975204317	0.0562252579844	-0.140046529643	-0.592880469949	0.00394472119832	-0.210884855827	0.467165569032	-0.0487219585608	0.0751391936457	0.371638649033	-0.0281448745697	0.303958959895	-22.0868805296	-1.57695256319	17.669306429
3	0.98743025693	-0.486372779816	-0.447355182753	1.25854801736	1.1297675815	2.955984757	-0.156147941978	-0.148179713124	0.0314105538258	0.297926355369	0.0254618097663	-0.0160604744801	0.13064043576	0.173148548031	0.135210761098	0.375646160166	-0.0491559508938	0.0339211069893	0.356393834531	0.0108954887666	0.309462103224	-19.5885500458	-21.5407645441	20.0980635736
4	2.20691778583	-0.414087897471	1.37828477179	5.31259134722	-0.726023690329	4.15535465796	0.17719404938	0.716064985478	-0.158657986345	-1.04945124221	0.0415189173567	0.614216836638	0.335115995044	-0.234857245751	-0.196139292217	0.436594690475	-0.0168250619831	-0.0238964964154	0.661060994801	-0.056196649657	0.339698055901	-28.7323166759	-27.0211804113	-16.2496446372
5	1.88114614417	-0.457636722344	0.656411616657	2.99863531936	-1.82914399818	4.05656975356	-0.0444810399025	0.0352885671475	-0.205792904313	-0.194895711427	-0.142160393441	-0.0699460601612	0.374187217235	0.270177457661	0.172353386273	0.295345900073	-0.00947801248513	0.0764298913051	0.371105581255	-0.0429656730618	0.253306265933	-15.2202658901	-35.6220234263	3.6140945925
6	1.16131402512	-1.21584839329	1.74455167806	1.61635161449	-1.80236840106	4.93457230249	-0.101253161144	0.00182318198796	0.169415982466	0.117908354071	0.0812618152816	-0.0230605343814	-0.690377377341	-0.306502684357	0.0144371056906	0.492309190118	0.0767774408535	0.063327672495	0.363603454039	0.0821460773453	0.388223158559	-15.5190964161	11.2587537503	-49.7254106894
7	3.02781224885	-0.839267960391	0.882225939219	3.46178455782	0.14088611095	3.86784004078	0.154821803529	0.282749756232	-0.120547921584	-0.382393659779	-0.00359116202808	-0.0645038724789	0.210051060105	0.0751176097417	-0.144572831534	0.364903144124	0.0877071800375	-0.0187884357471	0.331934661268	0.0722589133267	0.253889851082	-6.42801125286	-6.93306066897	-48.724128571
8	1.80621830299	-0.632301365184	0.298064050089	2.25099081746	-0.0313472248028	2.07988827602	0.114186559104	-0.0413469047237	-0.0775019888814	0.0313331047182	0.0540406365517	-0.0983125108287	0.206625926976	0.175407421654	-0.17026714338	0.332477260816	-0.0216908482802	-0.0392563978902	0.290687508298	0.0708401646529	0.290908570617	8.13240467037	-18.3064419587	-22.0653258225
9	0.209907380219	-0.10457196155	-0.562456541231	5.6312342292	3.24453059137	8.08800265783	-0.349012245104	-0.67877122499	0.276145434499	1.54492794589	0.303640268333	-0.308803331908	-0.00616670565596	-0.0107630970796	0.0214763500772	0.969519755925	0.0816571467584	-0.102424345064	0.614462400574	-0.0427870015375	0.567962935429	22.0123140113	51.5545205132	-15.1697052241
10	3.47660220131	0.181993198614	-0.561583082091	2.86057270635	0.299311419096	2.40979452666	-0.0238061343939	-1.06705189485	0.263034220946	1.11716352514	0.184531919418	-0.232204436695	0.0282029190958	0.217379424785	-0.306947674171	1.5674920029	0.132188459883	-0.226647370181	1.11645599585	-0.225446284585	0.653936572852	25.9924684183	52.5080395034	-4.17215772251
11	3.6365904464	-0.0328568312177	-1.48629191604	3.9381198363	1.55681442606	5.22569284779	-0.243841867993	-0.817868088853	-0.220050530626	1.44587720624	0.206568120557	0.276048933197	0.535101751014	0.111167887825	0.0328804594334	0.840543374791	0.110218497468	0.0831438494523	0.542292997634	0.0643146677552	0.484107544287	20.1421708098	34.9487717109	-21.095733268
12	3.00079741879	-0.437075619923	-0.0812037716253	7.82125597771	0.539980769862	3.3221665876	-0.0225068741198	-0.267789948123	0.496860330162	0.41398400225	-0.075255913748	0.571433279941	-0.349501272611	-0.132105502646	0.00810847567895	0.569483167663	0.0618738954658	0.00389338607339	0.395040266476	-0.0357983225396	0.459642664917	16.5535807661	49.0264996626	-30.095331211
13	1.95554864166	-1.46706000679	-1.22761884862	2.2331125193	3.26865330671	5.65626873645	-0.070741139217	-0.167037086796	0.125948097124	0.0170946454871	-0.145555192683	0.505967051869	-0.224003563521	-0.620571152166	0.256639171484	0.398606986395	0.025712009136	-0.00680770380309	0.434758449211	-0.0192878301481	0.722937294549	5.73307691094	41.5359844154	-43.8974747149
14	5.75618151183	-1.76339159313	-0.231761060969	6.17649114387	0.37636879571	3.82334998339	0.143426220134	0.474825837509	0.138318412537	-0.821158736225	0.0495677382935	-0.769091246958	0.119647096506	0.292686723419	-0.18431703286	0.386649495895	0.0474431506743	0.125811873312	0.375507997722	0.0481856634796	0.442426027769	38.6421979949	23.3774352871	-56.3744445162
15	8.29632243532	-3.78073928379	1.74532140512	1.94563456278	-0.759822342417	4.42018670442	0.300684132994	0.342421406693	-0.476227155557	-0.138504019335	-0.423274232097	-0.0522123555839	0.516820949616	0.664521070295	0.114755634553	0.478394411379	0.0386383662784	0.049933045839	0.300683312155	0.0444074449694	0.475022616978	38.7453056225	18.7048865699	-51.8975434497
16	2.73861939485	-1.56287860023	0.865507490197	3.29255970272	-0.776676566098	2.2281642131	0.13051788356	0.099647629503	-0.0756099335009	-0.643761964859	-0.126640707932	0.458909326558	-0.0483192287264	-0.105839882878	0.0134234322583	0.460013494348	0.0129568350013	-0.00278285800605	0.311879794892	0.00827984033242	0.42606342443	17.6407180896	34.0467018521	-57.7270930156
17	0.350462582617	-0.85503685174	-0.0448916500289	3.80253434497	-0.589320333082	3.94312873781	-0.0443709321951	-0.796537066035	0.112065805203	0.241598204335	-0.098351179392	1.33737296409	0.135814340239	-0.87462661617	-0.116688842309	0.343314238993	-0.0689872148421	0.191299115658	0.754169101247	0.0087992596718	0.560402002776	-32.9954979292	-20.4446199741	4.77724177151
18	1.05190970265	-0.908039213312	1.19520984357	4.03680379484	0.269828723785	1.94205587766	-0.12906310678	0.0365834195493	-0.313305293951	-0.0462571559719	0.0422719207933	0.846321759285	0.481566324267	-0.930769923924	0.0437933102203	0.335967718712	-0.155564074802	-0.0305772694987	0.590461311638	-0.0235438193204	0.426339412233	-29.0587612101	-19.3243610141	2.53058891053
19	3.22320993648	-0.69802359082	-2.1219753002	1.53293391394	-0.212991466596	1.6755852133	0.3930419295	-0.454387804591	0.542910133761	0.00770672448943	-0.357996457347	-0.134694463236	-0.519092045269	0.94125178294	-0.0573955804722	0.356402939057	-0.130622628088	0.0105817961436	0.461594546141	0.0572310727865	0.331612462752	4.69060852326	-2.60920521747	-25.8222591284
20	2.18072125299	-1.0120682661	-0.193176557584	1.74906470733	-1.98602753347	3.54581456827	-0.243765243288	-0.213733992307	0.295906215355	-0.443999829102	0.0396148107605	-0.430554160721	-0.160168904525	0.465329352364	0.281388669814	0.482864423034	-0.136710602577	0.112522219954	0.234560346217	-0.04703590004	0.412078665813	7.67893174726	-0.0708411502596	-28.7929143932
21	2.46583932428	-1.77974872079	1.06546493369	2.72536447977	1.72180596979	4.66042286907	-0.195591352345	-0.0566748429987	0.279494829218	-0.0162787678339	-0.0091284101152	-0.603862701396	-0.34427851487	0.572624957016	0.243471641488	0.453910889324	-0.0216755833602	0.129815477842	0.421504419992	0.16263679621	0.603426107519	31.5041321323	32.6412323772	-42.0719689118
22	1.43872579719	-1.33754829487	-1.27718833432	2.48543857305	-0.275248053097	3.92459238834	-0.133691324894	-0.734497829287	0.841641399376	0.0848298785289	-0.268996647031	-0.511296203823	-0.518748616761	0.831075702322	0.28412478032	0.457698383639	-0.12723121942	-0.115380752169	0.567613082616	0.104836033051	0.870872887788	34.720149103	36.5555455761	-41.7704433261

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 27 through 130 )	A	A	27 - 130	2 - 105
2	2	chain 'A' and (resid 131 through 246 )	A	A	131 - 246	106 - 216
3	3	chain 'A' and (resid 247 through 359 )	A	A	247 - 359	217 - 329
4	4	chain 'A' and (resid 360 through 428 )	A	A	360 - 428	330 - 398
5	5	chain 'A' and (resid 429 through 577 )	A	A	429 - 577	399 - 547
6	6	chain 'B' and (resid 27 through 206 )	B	B	27 - 206	1 - 180
7	7	chain 'B' and (resid 207 through 311 )	B	B	207 - 311	181 - 285
8	8	chain 'B' and (resid 312 through 577 )	B	B	312 - 577	286 - 551
9	9	chain 'C' and (resid 28 through 66 )	C	C	28 - 66	1 - 39
10	10	chain 'C' and (resid 67 through 147 )	C	C	67 - 147	40 - 110
11	11	chain 'C' and (resid 148 through 223 )	C	C	148 - 223	111 - 186
12	12	chain 'C' and (resid 224 through 301 )	C	C	224 - 301	187 - 264
13	13	chain 'C' and (resid 302 through 345 )	C	C	302 - 345	265 - 308
14	14	chain 'C' and (resid 346 through 381 )	C	C	346 - 381	309 - 344
15	15	chain 'C' and (resid 382 through 428 )	C	C	382 - 428	345 - 391
16	16	chain 'C' and (resid 429 through 577 )	C	C	429 - 577	392 - 540
17	17	chain 'E' and (resid 1 through 14 )	E	D	1 - 14
18	18	chain 'D' and (resid 1 through 14 )	D	E	1 - 14
19	19	chain 'F' and (resid 1 through 14 )	F	F	1 - 14
20	20	chain 'G' and (resid 1 through 14 )	G	G	1 - 14
21	21	chain 'H' and (resid 1 through 14 )	H	H	1 - 14
22	22	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

-
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