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- PDB-9f7l: Bartonella henselae NrnC bound to deoxy-pGG -

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Open data

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Basic information

Entry

Database: PDB / ID: 9f7l

Title

Bartonella henselae NrnC bound to deoxy-pGG

Components

3'-5' exonuclease
DNA (5'-R(P*DGP*DG)-3')

Keywords

HYDROLASE / DEDDy family / Dinuclease

Function / homology

Function and homology information

nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function

Biological species

Bartonella henselae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Mortensen, S. / Sondermann, H.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2025
Title: Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria.
Authors: Mortensen, S. / Kuncova, S. / Lormand, J.D. / Myers, T.M. / Kim, S.K. / Lee, V.T. / Winkler, W.C. / Sondermann, H.

History

Deposition	May 4, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 9, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	9f7l.cif.gz	838.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9f7l.ent.gz	574.9 KB	Display	PDB format
PDBx/mmJSON format	9f7l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/9f7l ftp://data.pdbj.org/pub/pdb/validation_reports/f7/9f7l	HTTPS FTP

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Related structure data

Related structure data	9f7dC 9f7gC 9f7jC 9f7mC C: citing same article (ref.)
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	#3 - Mar 2000 DNA Polymerase similarity (3)

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Assembly

Deposited unit

A: 3'-5' exonuclease

B: DNA (5'-R(P*DGP*DG)-3')

C: 3'-5' exonuclease

D: DNA (5'-R(P*DGP*DG)-3')

E: 3'-5' exonuclease

F: DNA (5'-R(P*DGP*DG)-3')

G: 3'-5' exonuclease

H: DNA (5'-R(P*DGP*DG)-3')

I: 3'-5' exonuclease

J: DNA (5'-R(P*DGP*DG)-3')

K: 3'-5' exonuclease

L: DNA (5'-R(P*DGP*DG)-3')

M: 3'-5' exonuclease

N: DNA (5'-R(P*DGP*DG)-3')

O: 3'-5' exonuclease

P: DNA (5'-R(P*DGP*DG)-3')

hetero molecules

193 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	71.334, 128.047, 128.710
Angle α, β, γ (deg.)	90.000, 94.820, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Components

#1: Protein	3'-5' exonuclease Mass: 23446.725 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BM1374165_00260 / Production host: Escherichia coli (E. coli) / References: UniProt: X5MEI1
#2: DNA chain	DNA (5'-R(PDGPDG)-3') Mass: 613.454 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Bartonella henselae (bacteria)
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 883 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.74 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M succinic acid (pH 6.5), 20% PEG 3350, and 20% xylitol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.2→47.57 Å / Num. obs: 115114 / % possible obs: 98.62 % / Redundancy: 3.6 % / B_iso Wilson estimate: 42.44 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.06394 / R_pim(I) all: 0.03926 / Net I/σ(I): 13.36
Reflection shell	Resolution: 2.2→2.279 Å / R_merge(I) obs: 0.7826 / Num. unique obs: 11364 / CC_1/2: 0.65 / R_pim(I) all: 0.4885

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→47.57 Å / SU ML: 0.3014 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2104	3916	1.75 %
R_work	0.1758	219277	-
obs	0.1764	115087	96.87 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.43 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→47.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13080	360	19	883	14342

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0071	13703
X-RAY DIFFRACTION	f_angle_d	0.8105	18604
X-RAY DIFFRACTION	f_chiral_restr	0.0532	2125
X-RAY DIFFRACTION	f_plane_restr	0.0091	2353
X-RAY DIFFRACTION	f_dihedral_angle_d	7.4747	1931

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 (%)
2.2-2.23	0.3069	129	0.3221	7378	X-RAY DIFFRACTION	90.51
2.23-2.26	0.3496	163	0.3153	7741	X-RAY DIFFRACTION	95.97
2.26-2.28	0.345	122	0.2987	7749	X-RAY DIFFRACTION	95.87
2.28-2.32	0.3007	121	0.2882	7703	X-RAY DIFFRACTION	95.88
2.32-2.35	0.3205	159	0.2911	7665	X-RAY DIFFRACTION	94.93
2.35-2.38	0.2804	134	0.2737	7639	X-RAY DIFFRACTION	93.82
2.38-2.42	0.3688	111	0.2721	7446	X-RAY DIFFRACTION	91.66
2.42-2.46	0.3285	121	0.2501	7101	X-RAY DIFFRACTION	87.65
2.46-2.5	0.2913	171	0.2505	7513	X-RAY DIFFRACTION	94.56
2.5-2.55	0.2768	137	0.2321	8101	X-RAY DIFFRACTION	99.4
2.55-2.6	0.3027	135	0.2219	8015	X-RAY DIFFRACTION	99.63
2.6-2.65	0.2267	170	0.212	8028	X-RAY DIFFRACTION	99.65
2.65-2.71	0.2913	123	0.2126	8120	X-RAY DIFFRACTION	99.55
2.71-2.77	0.2802	150	0.2018	8064	X-RAY DIFFRACTION	99.73
2.77-2.84	0.2714	132	0.2084	8077	X-RAY DIFFRACTION	99.66
2.84-2.92	0.2377	163	0.1962	7964	X-RAY DIFFRACTION	99.62
2.92-3	0.2297	125	0.1915	8085	X-RAY DIFFRACTION	99.39
3-3.1	0.2535	136	0.1845	8036	X-RAY DIFFRACTION	99.31
3.1-3.21	0.2306	145	0.1825	8001	X-RAY DIFFRACTION	99.21
3.21-3.34	0.2303	136	0.1714	8042	X-RAY DIFFRACTION	99.3
3.34-3.49	0.1625	140	0.1689	8021	X-RAY DIFFRACTION	98.96
3.49-3.68	0.1992	133	0.1462	7973	X-RAY DIFFRACTION	98.37
3.68-3.91	0.174	149	0.1506	7805	X-RAY DIFFRACTION	96.87
3.91-4.21	0.1504	155	0.1278	7727	X-RAY DIFFRACTION	95.89
4.21-4.63	0.1302	134	0.1276	7464	X-RAY DIFFRACTION	92.55
4.63-5.3	0.1899	139	0.1364	7807	X-RAY DIFFRACTION	96.54
5.3-6.67	0.2154	136	0.1689	8074	X-RAY DIFFRACTION	99.58
6.68-47.57	0.1573	147	0.1368	7938	X-RAY DIFFRACTION	98.33

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	4.65233828185	-2.88584123259	-0.119657946959	6.61715125071	1.72002626928	2.89625269801	0.0480656299263	0.028443710804	-0.0328534683079	-0.301051582159	-0.114982211442	0.305222041796	-0.293510580872	-0.399776479585	0.0546139823951	0.314325417726	-0.0125253813612	-0.0440876836215	0.31835687739	0.0269707153934	0.265937583004	23.8662829438	28.479271931	9.52773474512
2	1.84290110741	0.671737603958	0.719657535523	5.04600970804	1.27197700255	3.21750670775	-0.0732258558831	0.243067962338	0.185326774785	-0.477140018242	-0.0561329712554	-0.0937551776824	-0.526930780123	0.0744004191993	0.100265250371	0.296677218649	0.0237715617828	-0.0077600197005	0.378349761829	0.0368049430486	0.290639406348	30.8940777282	33.254177171	9.73534689391
3	2.58191501164	-0.590661533607	-2.33118142716	0.448768272042	0.517377459038	8.62933091424	-0.111652405001	-0.0580564873457	-0.244627010445	0.0457781158558	0.00184640343535	0.0991829772097	0.387122361989	-0.172692530258	0.109584983654	0.337943230206	-0.00388222507726	-0.0465929330959	0.237065835523	0.0154318606907	0.33396514948	30.8087116407	25.8679538593	23.9468022315
4	4.72903298334	-2.41606085363	-5.77321638333	3.34552350992	4.12248989991	7.72608614165	-0.304513436192	-0.124742704012	-0.410167250401	0.34931538508	0.165496009268	-0.0090624137262	1.2104015759	-0.737332102549	0.18513320721	0.440368364709	-0.0838807310776	-0.0712348395466	0.559917936282	-0.0433339799277	0.564391325039	19.3336325794	17.1030262473	14.0310844431
5	2.68810167071	0.906770217321	-1.23089177926	7.23159067321	7.76724223508	2.02331689491	-0.126173875115	0.183310738263	-0.557459841967	0.701966550081	-0.551037200596	1.16406484032	0.762292223896	-1.20170105306	0.705227322593	0.425969288906	-0.0468843536591	0.0321366011418	0.553758416776	0.0186816153997	0.652972941553	17.2318943043	21.9958535564	14.5210676534
6	5.0103839846	-0.688828083568	-2.0877234463	1.15281751155	0.790787845778	3.39512123782	-0.0517767689754	-0.0193639844182	0.177855924618	0.0133538623178	0.107269802947	-0.0312551831875	-0.285427726625	-0.0601940933503	-0.0593184386565	0.340292783884	-0.0177898565717	-0.0460192020573	0.249942070098	0.0215697874618	0.261846043507	36.6461826754	30.1080085581	27.3066689591
7	3.04439298156	5.67932357854	4.80351097446	2.00272598747	8.70282252532	9.17847410148	0.513840861634	-0.0883158789418	-0.291660603113	0.309116663246	0.244951992399	-0.885821972737	0.783660792223	-0.139817109961	-0.739695593808	0.421157734736	-0.0656247297742	-0.00203814997134	0.383610699064	-0.0435929327662	0.450676013874	30.3330267994	16.6615986556	18.7771892594
8	5.16070059704	-1.3746116899	0.222094146158	4.25327722265	-2.02158917469	7.0095367007	-0.0836421988316	-0.374150261356	-0.187896475111	0.224472839907	0.0639197952075	0.665373906823	-0.120163675799	-1.02737283049	0.0153727647197	0.349215113674	0.0613116049208	0.0498778415564	0.496117193907	-0.0508681309057	0.413957491084	14.1567164788	24.9961795807	63.4671206749
9	1.81802794561	-0.533379726926	0.640750120894	1.87531394974	-0.636170772272	2.59055748053	-0.0025433261981	-0.185982431351	0.140940350128	0.192077147445	0.0117605168405	0.141998167269	-0.172534351923	-0.0673030629551	-0.0111896383653	0.268814279915	0.00353422295314	0.00567279645335	0.282096433139	-0.0381866049184	0.262230720099	24.9576302397	23.4444144038	58.0784530996
10	2.28224850319	0.120831728234	-0.285939247902	7.77980049669	-1.51048681097	0.255030967273	0.0102439171333	0.226480818899	-0.16283665584	-0.199864394873	0.147840650496	0.34622711478	0.0574949758924	-0.0593714318961	-0.142233585757	0.31322350335	0.0173685151665	-0.00102591311146	0.309209877918	-0.00876060768061	0.196399269545	28.0783535973	9.99801894416	55.609641201
11	2.59837059403	0.733533956912	0.226272552938	8.55116811748	-4.06050188519	4.80564766783	0.0803033766161	0.431190784209	-0.34370076291	-0.802544157081	-0.123835610945	0.45891488338	0.40220387147	-0.221368875616	0.0206271740057	0.366020384344	0.0192502441792	-0.0799954317981	0.509856883374	-0.0529527103461	0.427961882702	16.1621977558	19.0747284648	47.4146747795
12	2.84326656444	0.674018672711	0.497340774301	2.09692372917	-0.0055666413568	0.389124063351	0.0949413839445	-0.288658825797	-0.0484219677917	0.355983201922	-0.0926910811584	0.080397112697	0.081136536767	-0.00636357592017	0.00187222244697	0.392284888891	0.0151830393865	-0.0181561602238	0.315241391595	-0.00363269543667	0.25779655529	34.1618192647	7.25173981509	60.2433476571
13	3.50516277506	-5.23084162086	6.31029058467	8.41387255615	-9.29522297906	2.0040977039	-0.231839734565	0.767959280929	0.475074785373	0.0926812416324	-0.663747852806	-0.341890812745	-0.159243686525	0.695560475256	0.961800876594	0.467085937587	-0.0723628838351	-0.0782175326295	0.460956525111	0.0623294949537	0.424853676859	28.1676150516	15.304605559	46.4217634602
14	2.21508012757	0.0641889988866	1.04843369303	3.15732318298	-1.33348669342	4.81271563717	0.026732243328	0.0715863611825	0.00393712035316	-0.348770372164	-0.0105378275421	0.384111070075	0.229942140791	-0.26904100003	-0.045290507418	0.342385281619	-0.0196975967384	-0.0158390299685	0.294480567949	-0.0577300898351	0.374524493856	25.0450140479	-20.0241857178	4.64628774047
15	0.99617083334	0.280927476291	-1.30107435079	4.2690614128	-1.86511348762	2.24292515217	-0.0917805638019	0.157582560179	-0.113803204263	-0.526764170888	0.183172433682	-0.116070830314	0.598565772235	-0.0550931176107	-0.0968930488615	0.34845681631	-0.0299604090283	-0.0571162327593	0.268228796744	-0.0523056230583	0.319543726745	32.272986785	-20.1857712061	0.529209186902
16	0.739672550159	-0.629337112824	-0.150426762003	7.09297586521	-1.0159804735	0.5200988698	0.0123717669625	0.0853410863018	-0.0186564185295	-0.116698193572	0.0402163298292	-0.174579259122	0.138904464546	0.0304979798456	-0.0708298426903	0.27987339917	-0.04559549037	-0.00609811880448	0.31330132767	-0.0606817772424	0.274517510234	36.0583507449	-11.5617721896	5.64810109716
17	2.02505680174	8.23818881065	-3.22508292656	5.7262360765	-2.78253318998	2.77047062972	0.543073183822	-0.939158066936	1.11517595101	0.706653809505	-0.45764900619	0.810896722896	-0.591100949622	0.00312266413658	-0.139264767549	0.38428372038	-0.00280105842118	0.0201164500316	0.377371414793	-0.0731826351279	0.511235889778	26.0092909622	2.7697260418	12.0244220029
18	8.18143965768	-7.99731479244	5.18174881351	8.02975992682	-5.57445648498	4.18132657587	-0.571108544663	-0.458989788139	0.612964356462	1.99979509221	0.414891385236	-0.358693095982	-0.761530401355	-0.0507833701433	0.306648310701	0.527758371638	-0.0673893707797	0.0825261993627	0.588585356608	-0.0690998237696	0.409829842648	20.0171833905	-16.0027703292	16.8928765197
19	5.92553968952	2.21959659445	-5.70237305837	2.01968186861	-7.11573994184	2.02517049411	-0.0317370362463	-0.538444574682	0.414717876335	0.674803226148	0.459036803843	0.870949104862	-0.658532376497	-0.815071626686	-0.356043287475	0.487266077881	0.0367612509794	0.016420286704	0.563872820798	-0.0297583555892	0.476612000028	18.0834591124	-14.3699122894	10.2791383264
20	6.01727283651	8.72075625906	-0.775474194272	2.10675292588	-1.69370004959	4.84055150284	-0.320991672865	0.590658596159	0.522199990694	-0.560831012981	0.349136966342	0.911862892467	-0.150764544904	-0.442619239902	-0.0457754386322	0.373883214318	0.0492587755435	-0.0809308060814	0.295915404265	-0.0350983830791	0.529060402039	28.5223756539	3.24162604278	-0.560026401118
21	4.26312704331	-2.16113312332	0.915713493186	5.8221910734	-2.08824923859	0.733909739759	0.0398851188155	0.18296093013	-0.102037509146	-0.403871803021	-0.0790789470287	-0.198389917492	0.163564063884	0.369564649418	-0.0151339564003	0.293869406956	-0.02663311577	0.0616876045671	0.328381944919	-0.0575692449616	0.292635587931	45.4913336358	-7.13678922511	7.81713973162
22	5.13952896494	3.34716270288	-4.5409832265	2.00351749206	1.99353934066	9.74435627867	-0.210904863364	-0.729088090804	-0.273183419629	0.481218985539	-0.876312157284	-0.846843000764	-0.00323000801468	0.572186966619	1.00478217489	0.444208810716	-0.036093308367	-0.00914478694658	0.340764265042	0.0694182858167	0.395044928365	30.7866060041	-11.2502158645	17.1654725967
23	2.12143279742	0.423176229504	0.809558735273	1.4557917476	1.06982115443	4.65769660513	-0.0775442426719	-0.186266979062	0.0941203964426	0.0559927153224	0.166955829244	-0.260778195374	-0.509230036756	0.429496951077	-0.0947755527077	0.323185330776	-0.018913822986	-0.0656462101537	0.359121273326	-0.0213873718716	0.321927246312	60.8371517688	33.5152926613	38.0350515971
24	1.57496853264	0.658237224027	0.798474224914	0.575780039234	0.675997034116	2.60230783926	-0.0187059526115	-0.152526418671	-0.290215471027	0.0867101040704	0.0717446235826	-0.283856666748	-0.129018824379	0.507224811833	-0.0503290452434	0.377173250584	-0.000588957347368	-0.0376089428697	0.395015193499	0.0165590710997	0.392758628575	58.6179403019	27.786089499	32.7901725522
25	3.24350362383	0.593902608709	-3.21012992014	6.1120380392	-2.25599307632	7.60600977999	-0.193307422934	-0.63304673157	-0.547671822737	0.149174588521	0.375331487659	-0.268066533898	0.11263890062	-0.729878054972	-0.17375222454	0.424978932765	0.0399143969232	-0.0690014813562	0.497708546531	0.0548595313706	0.454999012167	57.9404445139	21.2694793049	39.7133383285
26	5.21269537391	-3.98417471079	-2.09252171166	9.19305909668	3.09643070417	3.97164351014	0.0180694336006	0.364839491748	-0.703222398552	0.0751056412396	-0.177315307262	1.24570678846	0.343727373366	-0.747843618867	0.0808511140242	0.342713023207	-0.0866455521099	0.00723208885964	0.415726294177	0.0463466879724	0.451203928466	15.7852238743	-30.7893057313	54.0467644919
27	1.05418205167	0.132477179962	-0.779291902138	4.25331374134	0.146046834236	0.651874794395	-0.0620796619119	-0.1072845701	-0.0868096280494	0.134859962291	0.0700247149069	-0.012750184232	0.111727561843	-0.0552144277327	-0.0134789226484	0.35442584877	-0.0222641535755	-0.0404408670334	0.363083271773	0.0635345223146	0.331038858344	25.7187671813	-24.35717955	52.9277370408
28	2.17213248232	0.6776774719	-0.031496573253	0.720221288141	1.89803784262	6.63900812474	-0.0057191515371	0.153559473381	0.0238144383976	-0.00872375721369	-0.0339471879019	0.0634240926788	-0.166370536627	-0.115030197354	0.0208158388557	0.339085373053	-0.0186866996681	-0.0151145503347	0.251062234596	0.0461443431477	0.341193680526	29.6771199565	-21.7467756052	39.6434104404
29	6.43845768278	3.39095318437	6.67698037586	4.44314309818	2.5680036424	7.27392017121	-0.747475750383	1.20375475623	0.679909037655	-0.375623181404	0.731782561567	-0.357967873762	-2.05158612714	0.827576987993	0.0332447377834	0.777607099779	-0.0443311132335	0.0032013367874	0.834404833426	0.185360832475	0.926075452971	16.6868660158	-12.5309973794	40.403659603
30	5.34452425979	0.902499608524	4.9863597856	9.27151199579	7.98798503318	2.00934202225	-0.601874299969	0.0316392722122	0.0982478341187	-0.52283489578	0.189656284981	0.435718706095	-1.72381338061	-0.941248989563	0.43161557389	0.478439832162	0.0676351307096	-0.0206104961689	0.445319370693	0.0709329383177	0.47510110502	17.8270579577	-11.2266366566	56.8022682088
31	1.22137174445	0.218836905171	-0.601777106457	0.26668536386	0.210203294604	2.04418121699	-0.143106429154	0.0909069985459	-0.00861347659073	0.0526084772191	0.082273055791	-0.00110753042448	0.161969012625	-0.101043286288	0.0478821957371	0.422176846394	-0.00226857790933	-0.0584570372586	0.331582221367	0.071605356273	0.408982964496	32.1648995387	-24.281648481	39.2638094497
32	3.21957063388	-6.05159962129	-5.62432731394	2.00244503693	2.00387088594	9.83546323385	-0.121890207701	-0.270405011666	0.643508052831	1.24112587702	0.892303911043	-0.867816372949	1.13531029842	0.866372153951	-0.726223232479	0.509519963711	0.0996165926394	-0.0694410320379	0.4576105499	-0.032899790809	0.471428429946	28.4343591496	-12.5503050191	44.8495656807
33	2.74873263724	-0.0510080730303	-1.33231595726	3.62025106547	0.283529217525	2.08972026479	0.0785405481373	-0.739852092877	0.239825957997	1.01811730175	-0.187953896202	-0.838859545334	0.153155565449	0.861373488674	0.130401999816	0.92884084974	-0.0850381406066	-0.440163190644	0.796093776898	0.177909206817	0.765115736408	67.9473829359	-4.72032976557	74.1583429619
34	1.3401543094	0.0820535131927	0.358342214054	3.61233177552	-0.361245824301	0.633413996721	0.162374904861	-0.40945305642	-0.224108348233	0.989740231366	-0.134751823993	-0.557510535878	0.00714476330487	0.131869794683	-0.0155846777009	0.581857102566	-0.0340090955271	-0.22024972464	0.526631937533	0.118185615965	0.533013281479	58.3502497437	-5.56100125488	67.107019905
35	2.35672462991	0.369476059002	0.248035888665	5.70452698032	-0.614982646419	0.767102501946	0.169591906091	0.00395618138095	-0.0090148065129	0.250928368859	-0.174520077626	-0.230622458688	0.0305508160783	0.151646360532	0.0683858817129	0.324287980414	-0.00386923691333	-0.117861785413	0.436671577435	0.0279765897429	0.318439803447	55.9427141872	5.4831700808	58.9097887098
36	2.25269841177	0.64469765255	-0.0898342654114	8.30681132732	-0.0510053240209	-0.0232191454878	-0.102865456893	0.403168052509	0.0263198929241	-0.256184857325	-0.0156760815883	-0.750672334455	0.0270208808393	0.267296540109	0.0754011871964	0.549349195279	0.0494296498203	-0.189402204515	0.716022125022	0.0497935892492	0.752495474097	68.6733622964	-5.74536201992	56.9911189933
37	2.17796564313	1.22995114437	-0.542706947516	3.59650473807	-0.887336546841	0.26571398006	0.17958449317	-0.238669270897	-0.175915812513	0.535918532102	-0.197857793788	-0.310229774311	-0.110042885099	0.274052439609	-0.00065694327874	0.435008389567	-0.00481429087042	-0.0708518847202	0.39644356584	0.00192018292618	0.272453166964	49.3096738663	9.68079898699	60.9229287862
38	1.79111644787	-1.93442348714	-1.85776653719	4.62470687222	1.38231961712	2.08358277172	-0.227144058798	0.307556909979	0.247243347272	-0.859577003086	-0.544317987345	0.806758930112	-0.052732494818	0.394554064423	0.769373059815	0.507737206026	0.0591505419097	-0.124137118517	0.435091490565	0.0770538842936	0.609422897402	57.0668760392	-3.18635403668	52.9144199667
39	2.64538186646	-1.73287519304	1.4556962417	1.20021368711	-0.972398844933	0.84568117123	0.106069088602	0.779176126898	-0.104270059247	-0.31268070401	0.0754432058737	-0.854853124849	0.305228305552	0.890610075662	0.00742581563986	0.581147254251	-0.0534195571996	0.224338512292	0.685347069362	-0.0896215040664	0.793971304295	74.1902874563	9.32657299164	-3.93997267814
40	2.43587228255	0.223156557109	0.299477575517	3.58737360032	0.974674873008	2.36457231435	-0.121653229767	0.211289005614	-0.0685969669676	-0.699684288839	0.23901241723	-0.534664669519	-0.0978621803364	0.291187194207	-0.0876717594702	0.369516062388	-0.0808572313988	0.0913403995829	0.366029722574	-0.0506183818551	0.448433004433	63.322029285	10.26447407	1.56614981079
41	1.58977878867	0.507858472085	-0.325929640981	8.57858174606	-2.48472692544	1.36799948729	-0.0417556544994	-0.176808050662	-0.180280468734	-0.0861960689872	0.00680048440738	-0.449833371194	0.012581617519	0.263577506478	0.043960118375	0.258053113052	0.0137708712272	0.0183442589196	0.37064711649	-0.0860390825577	0.40497987772	60.020909387	-0.799568111324	9.44843171401
42	3.35423095621	-1.15801622958	1.14086851423	4.83243612388	0.0305323935987	1.6956309678	0.0178915590338	-0.17825579198	-0.345751094755	0.344858868838	-0.0165639915053	-0.267501932844	-0.00847878658011	0.524263144091	-0.0059285161861	0.36368622722	-0.0440969149694	0.0295526553045	0.597688151918	-0.0517885296366	0.596422619987	72.0386600101	10.825629433	13.0413668613
43	2.40026716737	-0.13918197021	-0.102290083744	3.69665278911	-0.354597948959	1.69077351968	-0.121575051738	0.0723602192381	-0.016308467381	-0.362737126557	0.0555464353305	-0.533817988509	0.111944348302	0.28950156093	0.0704585050893	0.303068353731	-0.0314762588593	0.0377868964127	0.315992757086	-0.0426379622935	0.321024094254	53.9174892545	-5.20229961151	6.39714258325
44	0.574347320003	-0.302128742483	0.993059357429	2.0041000596	2.46567714515	2.48656563551	-0.390425633067	-0.326659842397	0.352793454645	-0.431902501788	-0.126044781857	1.10719852552	-0.260151162852	-0.304433468199	0.526705352319	0.375406838671	-0.024386085284	-0.0948139894601	0.457559628704	-0.0659162593329	0.636598912591	60.0019452349	7.89196073972	15.4601671635
45	1.10551796749	0.127114508234	-0.814473381693	1.02360373984	0.918124259983	4.04584584691	-0.0753965997858	-0.0436968344683	-0.234318470201	0.162544231217	0.102921434497	-0.530730393626	0.561124452814	0.524275854865	-0.0132085637409	0.365129312665	0.0946430624642	-0.0616177213645	0.421237111443	0.0180823150271	0.616365062376	61.8798326609	-29.5965104961	29.9443503479
46	7.48802067556	-0.721146627038	-5.60692191914	1.9524370601	1.00892816766	4.75781389144	0.0360989970097	0.429600333391	1.38853841747	-0.250305175943	-0.0247183638827	-0.648674944228	-0.615881859069	1.71183697829	0.0560129311234	0.494376173151	-0.0437678319268	-0.121529291256	0.866887331669	0.0824479280083	0.829638087791	69.0997527236	-15.643516282	37.4760439959
47	3.98184631134	-1.99402946791	3.55672671848	3.73148019505	-5.43495088114	8.13058463686	-0.502453683542	-0.0336425524638	0.473301585831	0.635490744928	-0.0123157026448	-0.948849800818	-1.6929824331	0.910436692509	0.6186498155	0.54133747016	-0.00997386355086	-0.103176034201	0.520922280816	0.0201297881891	0.941741079321	71.653752528	-21.8018230487	24.3997873933
48	2.59157556897	-0.740380052459	0.274251233474	1.3343441443	0.711739090209	3.36388378788	-0.104596628802	-0.0950272385436	-0.130565558843	0.350772803444	0.0766726460757	-0.49698554722	0.398913748735	0.398671674259	0.0285098798431	0.431187775981	0.0135599850601	-0.0719143300563	0.320925603622	0.057662696702	0.52585077503	51.1989937292	-25.127160625	41.0171732211
49	2.66491038697	2.97244635802	-3.4354673431	3.33813289685	-3.38059980157	2.00247117155	-0.263873086154	0.423948749024	0.597405930132	-0.011732561275	0.485391603934	-0.0532130087302	0.0343407448555	-1.60630140404	-0.20619113667	0.365069258808	-0.0191113524291	-0.0556128511886	0.64699536735	0.0529194368888	0.485319402053	59.334516891	-16.5221254707	28.7215052818

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 1 through 54 )	A	A	1 - 54	1 - 54
2	2	chain 'A' and (resid 55 through 80 )	A	A	55 - 80	55 - 80
3	3	chain 'A' and (resid 81 through 125 )	A	A	81 - 125	81 - 125
4	4	chain 'A' and (resid 126 through 145 )	A	A	126 - 145	126 - 142
5	5	chain 'A' and (resid 146 through 158 )	A	A	146 - 158	143 - 155
6	6	chain 'A' and (resid 159 through 206 )	A	A	159 - 206	156 - 203
7	7	chain 'B' and (resid 603 through 604 )	B	B	603 - 604
8	8	chain 'C' and (resid 1 through 20 )	C	C	1 - 20	1 - 20
9	9	chain 'C' and (resid 21 through 80 )	C	C	21 - 80	21 - 80
10	10	chain 'C' and (resid 81 through 126 )	C	C	81 - 126	81 - 126
11	11	chain 'C' and (resid 127 through 158 )	C	C	127 - 158	127 - 158
12	12	chain 'C' and (resid 159 through 206 )	C	C	159 - 206	159 - 206
13	13	chain 'D' and (resid 603 through 604 )	D	D	603 - 604
14	14	chain 'E' and (resid 2 through 54 )	E	E	2 - 54	1 - 53
15	15	chain 'E' and (resid 55 through 80 )	E	E	55 - 80	54 - 79
16	16	chain 'E' and (resid 81 through 109 )	E	E	81 - 109	80 - 108
17	17	chain 'E' and (resid 110 through 126 )	E	E	110 - 126	109 - 125
18	18	chain 'E' and (resid 127 through 145 )	E	E	127 - 145	126 - 144
19	19	chain 'E' and (resid 146 through 158 )	E	E	146 - 158	145 - 157
20	20	chain 'E' and (resid 159 through 175 )	E	E	159 - 175	158 - 174
21	21	chain 'E' and (resid 176 through 206 )	E	E	176 - 206	175 - 205
22	22	chain 'F' and (resid 603 through 604 )	F	F	603 - 604
23	23	chain 'G' and (resid 1 through 126 )	G	G	1 - 126	1 - 126
24	24	chain 'G' and (resid 127 through 206 )	G	G	127 - 206	127 - 206
25	25	chain 'H' and (resid 603 through 604 )	H	H	603 - 604
26	26	chain 'I' and (resid 1 through 20 )	I	I	1 - 20	1 - 20
27	27	chain 'I' and (resid 21 through 80 )	I	I	21 - 80	21 - 80
28	28	chain 'I' and (resid 81 through 126 )	I	I	81 - 126	81 - 126
29	29	chain 'I' and (resid 127 through 135 )	I	I	127 - 135	127 - 135
30	30	chain 'I' and (resid 136 through 145 )	I	I	136 - 145	136 - 145
31	31	chain 'I' and (resid 146 through 206 )	I	I	146 - 206	146 - 206
32	32	chain 'J' and (resid 603 through 604 )	J	J	603 - 604
33	33	chain 'K' and (resid 1 through 20 )	K	K	1 - 20	1 - 20
34	34	chain 'K' and (resid 21 through 80 )	K	K	21 - 80	21 - 80
35	35	chain 'K' and (resid 81 through 126 )	K	K	81 - 126	81 - 126
36	36	chain 'K' and (resid 127 through 158 )	K	K	127 - 158	127 - 158
37	37	chain 'K' and (resid 159 through 206 )	K	K	159 - 206	159 - 206
38	38	chain 'L' and (resid 603 through 604 )	L	L	603 - 604
39	39	chain 'M' and (resid 1 through 20 )	M	M	1 - 20	1 - 20
40	40	chain 'M' and (resid 21 through 80 )	M	M	21 - 80	21 - 80
41	41	chain 'M' and (resid 81 through 126 )	M	M	81 - 126	81 - 126
42	42	chain 'M' and (resid 127 through 158 )	M	M	127 - 158	127 - 158
43	43	chain 'M' and (resid 159 through 206 )	M	M	159 - 206	159 - 206
44	44	chain 'N' and (resid 603 through 604 )	N	N	603 - 604
45	45	chain 'O' and (resid 0 through 117 )	O	O	0 - 117	1 - 118
46	46	chain 'O' and (resid 118 through 135 )	O	O	118 - 135	119 - 136
47	47	chain 'O' and (resid 136 through 158 )	O	O	136 - 158	137 - 159
48	48	chain 'O' and (resid 159 through 206 )	O	O	159 - 206	160 - 207
49	49	chain 'P' and (resid 603 through 604 )	P	P	603 - 604

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-Yorodumi

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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

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Yorodumi