PDB-7pd7: Crocagin methyl transferase CgnL

ID or keywords:

Entry

Database: PDB / ID: 7pd7

Title

Crocagin methyl transferase CgnL

Components

Methyltransferase

Keywords

BIOSYNTHETIC PROTEIN / RiPP / crocagin / CgnL / methyl transferase

Function / homology

Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein

Function and homology information

Biological species

Chondromyces crocatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Zheng, D. / Koehnke, J.

Funding support

European Union, 1items

Citation

Journal: Nat.Chem. / Year: 2023
Title: Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis.
Authors: Adam, S. / Zheng, D. / Klein, A. / Volz, C. / Mullen, W. / Shirran, S.L. / Smith, B.O. / Kalinina, O.V. / Muller, R. / Koehnke, J.

History

Deposition	Aug 4, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 17, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 22, 2023	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2	Mar 22, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Apr 12, 2023	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5	Feb 28, 2024	Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 2.0	Oct 1, 2025	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_entry_details / pdbx_validate_close_contact / struct_conn Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7pd7.cif.gz	686.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7pd7.ent.gz	478.1 KB	Display	PDB format
PDBx/mmJSON format	7pd7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7pd7_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7pd7_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7pd7_validation.xml.gz	51.4 KB	Display
Data in CIF	7pd7_validation.cif.gz	65 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pd/7pd7 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/7pd7	HTTPS FTP

-
Related structure data

Related structure data	6zsuC 6zsvC 8a2nC 3e23S 7aox PDB Unreleased entry C: citing same article (ref.) S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Methyltransferase

B: Methyltransferase

C: Methyltransferase

D: Methyltransferase

hetero molecules

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

1

A: Methyltransferase

hetero molecules

defined by author
Evidence: gel filtration
28.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Methyltransferase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Methyltransferase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Methyltransferase

hetero molecules

defined by author
28.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.947, 128.117, 94.295
Angle α, β, γ (deg.)	90.000, 90.393, 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

#1: Protein	Methyltransferase / Crocagin methyl transferase CgnL Mass: 27756.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chondromyces crocatus (bacteria) / Gene: CMC5_025500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K1EC20
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Mass: 384.411 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12 M Monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose, N-Acetyl-D-Glucosamine) 0.1 M Buffer System 1 (Imidazole, MES monohydrate) pH 6.5 37.5 % v/v Precipitant Mix 4 ...Details: 0.12 M Monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose, N-Acetyl-D-Glucosamine) 0.1 M Buffer System 1 (Imidazole, MES monohydrate) pH 6.5 37.5 % v/v Precipitant Mix 4 (12.5% each of MPD (v/v), PEG 1000 (w/v), PEG 3350 (w/v))

Crystal

Density Matthews: 2.26 Å³/Da / Density % sol: 45.59 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Monosaccharides (D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose, N-Acetyl-D-Glucosamine) 0.1 M Buffer System 1 (Imidazole, MES monohydrate) pH 6.5 37.5 % v/v Precipitant Mix 4 ...

-
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 PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.96→47.15 Å / Num. obs: 69598 / % possible obs: 100 % / Redundancy: 9.2 % / B_iso Wilson estimate: 29.7 Å² / CC_1/2: 0.997 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.96→2 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4446 / CC_1/2: 0.519

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Starting model: 3.0E+23 / Resolution: 1.96→47.15 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2316
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2227	3542	5.09 %
R_work	0.1853	66010	-
obs	0.1872	69552	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 38.25 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→47.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7619	0	146	402	8167

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0118	7946
X-RAY DIFFRACTION	f_angle_d	1.264	10782
X-RAY DIFFRACTION	f_chiral_restr	0.0521	1176
X-RAY DIFFRACTION	f_plane_restr	0.0075	1420
X-RAY DIFFRACTION	f_dihedral_angle_d	18.5858	1160

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 (%)
1.96-1.99	0.3523	120	0.2934	2619	X-RAY DIFFRACTION	99.89
1.99-2.02	0.3147	143	0.2793	2656	X-RAY DIFFRACTION	99.86
2.02-2.05	0.2608	125	0.2657	2662	X-RAY DIFFRACTION	99.89
2.05-2.08	0.3013	128	0.2596	2622	X-RAY DIFFRACTION	99.93
2.08-2.11	0.314	155	0.256	2609	X-RAY DIFFRACTION	99.93
2.11-2.15	0.3005	190	0.2441	2637	X-RAY DIFFRACTION	100
2.15-2.19	0.2936	161	0.2292	2570	X-RAY DIFFRACTION	99.96
2.19-2.23	0.2713	125	0.2328	2634	X-RAY DIFFRACTION	100
2.23-2.27	0.2598	160	0.2152	2688	X-RAY DIFFRACTION	99.96
2.27-2.32	0.2653	134	0.2148	2577	X-RAY DIFFRACTION	100
2.32-2.38	0.2607	137	0.2092	2645	X-RAY DIFFRACTION	99.93
2.38-2.44	0.264	130	0.2044	2635	X-RAY DIFFRACTION	100
2.44-2.5	0.2582	158	0.2049	2623	X-RAY DIFFRACTION	100
2.5-2.58	0.2715	141	0.1951	2653	X-RAY DIFFRACTION	99.96
2.58-2.66	0.2386	156	0.1897	2598	X-RAY DIFFRACTION	100
2.66-2.76	0.1878	175	0.1862	2630	X-RAY DIFFRACTION	100
2.76-2.87	0.2358	144	0.1761	2634	X-RAY DIFFRACTION	99.96
2.87-3	0.2282	128	0.1812	2651	X-RAY DIFFRACTION	100
3-3.15	0.19	112	0.1654	2698	X-RAY DIFFRACTION	99.96
3.15-3.35	0.2238	128	0.1665	2637	X-RAY DIFFRACTION	100
3.35-3.61	0.1769	140	0.1595	2641	X-RAY DIFFRACTION	100
3.61-3.97	0.1745	135	0.1447	2657	X-RAY DIFFRACTION	99.96
3.97-4.55	0.1679	131	0.1428	2697	X-RAY DIFFRACTION	100
4.55-5.73	0.1823	141	0.1613	2647	X-RAY DIFFRACTION	100
5.73-47.15	0.2399	145	0.2091	2690	X-RAY DIFFRACTION	99.86

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	2.84095568654	0.532013446287	-0.237549149743	1.98142203594	0.154272350757	3.33101714822	-0.0687248971122	0.403307969482	-0.348539309388	0.634986987949	0.356057339974	0.516823099717	0.427396813991	-0.0160105362043	-0.0205097276857	0.405891707438	0.0307457362358	-0.040720001543	0.412068855471	-0.0352763661321	0.376703116316	13.8634573612	34.9711068924	53.7943485851
2	4.06786605033	-0.764804673996	-0.526585868831	3.34628214034	1.35661129886	5.62842717256	0.0919107756903	0.0264085055041	-0.315418381279	-0.297030032559	0.0708185132757	-0.25178677917	0.194937837444	0.737701570739	-0.00958162665886	0.397177105531	0.0639628839674	0.0732313620925	0.261925649806	0.0322852110528	0.479691687584	23.551931468	31.6069284607	72.6655030993
3	1.91223416874	-0.14168194115	0.798150354067	0.955415876881	-0.527074421189	3.77398355451	-0.0520365522731	-0.329488397212	-0.356520590711	0.318451149309	0.135453552821	0.316354162694	0.184129884692	0.017989093318	-0.0456418237398	0.341974612192	0.0331836807994	0.102911274406	0.232415267893	0.081829943035	0.376219810677	12.6752621982	33.0208122465	73.7724401808
4	2.66322959405	-0.019967410081	0.86853488811	1.31796108309	-0.201549550081	3.72268759032	-0.0500134593858	-0.0302551471507	-0.184563090848	0.0933452737349	0.0634628200554	0.245401895982	-0.018703440114	-0.410213075862	-0.0370502412027	0.24225092309	0.0251660636098	0.0472292645	0.257449151544	0.0313165778927	0.320296249788	6.51587900571	38.8383674751	68.6722352154
5	0.681052947997	-0.495088046296	-0.197152001237	0.469314261312	0.341420411227	1.63459732633	0.0135030939901	-0.0726913507301	0.0831968618779	-0.00722861998247	0.12997286791	0.0814275181682	-0.103123286585	0.127746693626	-0.0437695754746	0.278484300339	0.0152579027868	0.00157393337472	0.244523647811	0.0159782709917	0.2871549317	21.0120812878	44.9897332245	65.0085409743
6	1.15510628131	1.30534205498	0.094472980586	1.94290246331	1.3124870063	2.30055573426	0.0183449490753	0.126376705902	-0.200672482364	0.290892238819	0.470299910641	-0.449230202071	-0.191881873869	0.198005750733	-0.0113911826139	0.319086143056	-0.00480774887936	-0.0197170993357	0.296863873749	0.0310939036226	0.264876196152	22.722179273	37.2466621625	48.2432238016
7	0.352147570777	0.404820261375	0.893923615376	2.12765954541	1.88614536385	2.32464060484	-0.0414150187064	0.0312658480396	0.107901249325	-0.000671933181416	-0.0432404598152	0.41283693742	-0.00842598652175	-0.00714673083471	-0.00575947213417	0.2915791939	-0.00402857938667	-0.0165430745591	0.305886807544	0.0151222554647	0.314011381939	17.9193546581	39.4184139848	46.6434830813
8	1.63047150207	-0.618352136398	-0.310890446222	2.17161550732	0.236739957264	3.14415630272	0.044543919484	-0.109274978185	0.122242120257	0.310683449768	0.045934052359	-0.0251044835141	-0.579277000261	0.367351131659	-0.0755057113692	0.365766904757	-0.0312056666492	-0.00281223897004	0.281824691057	-0.015943580452	0.300744088951	26.4966602215	51.353751538	71.406983763
9	1.81738472351	-0.471107908031	-0.80759985044	1.62225128912	0.332545991781	3.24102290283	-0.352005360542	-0.349570049271	-0.559143302099	0.201087762174	-0.127605606269	0.0655479612956	0.0134957751569	0.387554393126	-0.0750802593022	0.268047697033	0.0155051304404	0.00582887580784	0.376088468751	0.0345337325923	0.328684376241	29.3790126054	42.0540794532	72.210519461
10	3.6573469139	-0.12986689822	-0.113104046308	2.65641313879	-0.425955615464	3.9113646994	0.260725259148	0.46198199769	-0.102635151458	-0.167370631677	-0.480312568345	0.356173008888	-0.220984223646	-0.787758854052	0.0531516209527	0.456970237768	0.0880877793872	0.0288261617512	0.590107903589	-0.0751844917251	0.351703529908	-6.81146275934	71.1541793476	122.982642507
11	4.67429725424	0.0217912965139	-1.49405635147	4.31297713917	1.67426433105	6.25953335907	0.0871326334285	-0.187833899282	0.778364547096	0.248770551	0.0618463834093	0.350181350771	-1.19520193716	-1.08862591811	-0.0232401812501	0.513366361783	0.135363401554	-0.0207017516679	0.425220398453	-0.0343017708407	0.454181893712	-3.73209210343	83.3337936428	104.854833964
12	2.41038890646	0.668728415225	-0.0939283307412	1.77838594436	-0.381004953562	3.68258617233	-0.0736541387841	0.143951267649	-0.0145806516704	-0.129624851448	0.0178697411025	0.344038577942	0.13476048806	-1.02514741885	0.0383679715994	0.202081341476	-0.0367395749421	-0.0226933184887	0.462864487389	-0.0817112377548	0.259998302987	-6.71797498995	68.2110627637	105.955296436
13	2.49222352431	0.250859026668	0.497509610018	2.10588014621	-0.497191874177	4.49917903608	0.0279052079504	-0.0239891451048	0.0660510662621	-0.0949200571101	-0.141350102008	0.0117633873545	0.0607852694111	-0.201088806278	0.142081343582	0.199634425463	-0.0165791614453	0.0128776120282	0.262585063182	-0.0315411424272	0.241527460489	7.01653263728	69.7133701904	106.805709644
14	2.53887901374	0.182063011995	-2.37371904679	1.02473698474	1.14745118145	4.66360770279	0.30839267682	-0.153697226993	0.31337053132	-0.0383635434935	0.26590691946	-0.0882672143459	-0.548702367186	0.143720939431	-0.430310785614	0.349914378376	-0.00655387199365	0.0284150397958	0.24410300167	-0.00463270753573	0.301566495035	4.28158086183	83.2823299714	125.651776096
15	1.75784545415	-0.448248400179	-2.52840165638	0.769074435764	0.999180234727	3.8424925856	0.0380078725706	0.0773317093576	0.0400449282021	0.0314343894764	0.0641693738253	-0.0631371614424	0.0257120886679	0.17776829682	-0.0584101634383	0.283689873927	-0.00122704500944	-0.0436398067388	0.238781193612	-0.00978629962251	0.249361245789	-0.870644426174	74.4531305838	130.220103788
16	1.79765399725	-0.716405921888	-1.8652782143	2.11581305251	1.2036518557	4.18617302031	0.0704894482154	-0.0535938860947	0.0114865330253	-0.0695152217994	0.222676395753	-0.13674441543	-0.428827920295	0.784051415389	-0.266551132631	0.271750541986	-0.0886902158772	0.0351893710991	0.324997549673	-0.0606561763702	0.309067816485	15.1123458521	75.4301748618	106.939074817
17	1.32321223156	0.636585623481	-1.80260415602	1.62009698783	0.0601467252743	5.29042809804	-0.029184537389	0.193496421291	0.278487878055	-0.864768237576	-0.15982474167	0.179618530362	-1.67576219957	0.185881299706	-0.415335974802	0.691623833619	-0.0779700023585	-0.00419013958061	0.33187193393	-0.0191638436826	0.409223326396	8.22963495797	87.3492181229	110.566378067
18	1.68437597489	0.179240250208	-1.98329098031	0.438298100153	1.08335744163	6.15195628496	-0.0829469075167	0.234319952021	0.330853851736	-0.345758595949	-0.394738744246	0.277594656076	-0.859301585644	-0.594576573557	-0.256612434641	0.262801594289	-0.0662947892611	0.0372560243302	0.319759494423	-0.00764552153748	0.301851630148	10.4798105527	74.7196029236	96.6503264557
19	4.28791963538	1.22720368476	-0.597102284216	4.72799471854	0.109049218224	5.79194263337	-0.183132339954	0.336062216321	0.404190217934	0.440582771478	0.0949853035594	-0.123794200105	-0.710722516607	-0.00462896152521	-0.00869824067723	0.37821274179	0.0228468602916	-0.0562485766485	0.341047238389	-0.000284884468827	0.333369540027	6.13093579937	78.0969120286	56.2018951607
20	4.62638145155	0.214534819783	-0.133947316974	4.42262820015	-1.31515050386	6.24729587272	0.128986389449	0.0541249583818	0.834352560095	0.0356608813188	0.13682569295	0.663320030097	-0.785463526072	-0.403629937697	-0.0416755326463	0.455561912696	0.0978850825517	-0.0356310990516	0.306081939931	-0.0188428157271	0.477105065458	-4.89237069772	82.3011316001	74.1722049865
21	2.45027275991	0.288484913804	-1.03081608281	1.8911704105	0.170887767155	5.27550546091	-0.105138184875	-0.300399655171	0.395406587685	0.284797546937	0.0718184396205	-0.403187306337	-0.557987109976	0.149237662124	-0.0583412634483	0.363416694573	0.00831255390345	-0.082493146001	0.328176498757	-0.0491212312265	0.391182230984	5.88834800264	81.1883216434	75.9909517434
22	2.40255177104	0.56506590388	-0.584706184931	1.37067656976	-0.496265794993	3.11408963199	-0.0657907744297	-0.106758183589	-0.0134181217758	0.136995316467	0.00648587105199	-0.232186549278	-0.0513745727249	0.268305792339	0.0831206019014	0.234231661018	0.0448478251416	-0.0410212680848	0.226705581432	-0.0157125591018	0.226205674353	7.11862267292	70.7450509532	72.2922735104
23	1.06592900922	0.112272676391	-0.33667119145	1.92062405219	-1.57429615678	3.99030484499	0.0932475290559	-0.0334838051768	0.198636380439	-0.234703688926	0.199914058394	0.190803558904	0.0709454832914	-0.234604818274	-0.179687767769	0.267956541784	0.0246793423423	-0.000403875247995	0.311180143202	-0.0420958420833	0.277150955831	-10.1154815231	74.4605127152	53.8441391648
24	0.930701656284	0.616600367611	-0.215703587308	1.77635923335	-1.67605853293	2.3580431523	0.0207077123513	-0.0587317970653	0.0365206245416	-0.160381616074	0.0220103479543	0.265963457749	0.24522170644	-0.0138358472774	0.0259862021885	0.249381414353	0.0125922386147	-0.0130406404417	0.267701040811	-0.0122747739313	0.245297202974	-0.0911720978385	74.8838826279	49.4218999324
25	1.41128059103	0.0585698375709	0.554633097729	1.75734298761	-1.42058416928	3.84573714667	-0.119064041058	-0.0473718955365	-0.282282002452	0.100355450855	0.103449372326	0.188397094267	0.697469224614	-0.469843607273	-0.0255676794976	0.29791676952	-0.0220552743619	0.0263595541698	0.277573138835	-0.00648728967209	0.2924806371	-7.64057416815	62.318504889	73.1546224965
26	0.731482795657	0.194133012654	1.37126902474	0.492502738316	-0.165963687248	5.48831455842	-0.304759523939	-0.390778144516	0.332280468687	0.164950984029	0.0261044352593	0.238008942984	-0.381587498504	-0.661082577273	-0.12013169495	0.337426742947	0.0463536860222	-0.00946086099225	0.396612504152	0.00977054025597	0.308400019316	-10.7006339086	71.6127022172	73.6536885139
27	5.82232414044	-3.68125963684	-0.793624095136	4.17185949462	-0.193880730588	2.86699898268	0.197337631499	-0.101399644891	-0.057419053345	-0.0536500870706	-0.158962608204	0.00259798678887	0.524656849129	0.40320734784	-0.0566432325642	0.480391130959	0.0148385305209	-0.0344915984438	0.40933994088	0.0406931684623	0.323848639481	25.9522901338	42.479546591	121.451999152
28	5.0523186717	-0.639727867664	1.94599686655	3.60307791977	-0.531321612512	7.30264711158	0.0272200058897	-0.168845917658	-0.665897389512	0.247235702869	0.246117379962	-0.295166817974	0.770020865805	0.492891028863	0.0289505727	0.363361666069	0.112094294862	-0.00913093813554	0.289836191238	0.0307063672371	0.421950137909	22.8413868933	31.1681268844	102.66944078
29	2.48507001778	-0.0240109189476	-0.582407693064	1.94450829034	1.32258174286	5.50229208336	0.0518312832042	0.281357350064	0.0825015561027	-0.126060149525	-0.0693425663102	-0.235843711437	0.0843165547923	0.56461448877	-0.105986686579	0.215157677596	0.0305594954566	0.0439869183159	0.384110369817	0.0656942746513	0.320250049846	26.5172218782	41.9926360172	102.140247193
30	5.23020247799	-1.50367443525	-2.40302008993	2.88022157574	0.566143411129	6.39392014555	0.111439523397	-0.175078306971	-0.0113551003534	0.240428392305	0.191284856299	-0.580510236316	-0.0393446542142	1.59489208572	-0.247635356058	0.223835339826	-0.0891998629442	-0.047660835011	0.536407183567	0.035419761961	0.39197463628	32.226652901	46.4171065765	112.427249188
31	2.02780434449	0.358887961554	0.282283864842	1.68358802872	1.16070384011	4.55679770013	0.152910524591	0.409266266177	0.620293316153	-0.067182382432	-0.158873250159	-0.0427670809521	-0.485973794256	0.70881796094	-0.111311656604	0.296631936703	-0.00995746775006	0.071527197611	0.334216105638	0.120729930727	0.359525866259	21.7150892455	51.7180707621	103.545989236
32	2.31485173621	-0.301930607837	-1.21376455874	1.20198409254	0.723565713543	4.57913657115	0.182352762684	0.143169916953	0.144769720885	-0.0288253814545	-0.0782394786068	-0.0734766228092	-0.115527954359	-0.0828171603555	-0.00260064528365	0.230954034695	0.00903541402317	0.00743546459088	0.248887351934	0.0643965991374	0.27031608693	12.1679791792	44.731745691	105.321896389
33	3.01699267006	-0.219317486051	1.98504190362	0.651346175717	-0.607684299119	4.10633605684	0.342290643561	-0.0978901639933	-0.324534580746	-0.0709765107625	0.181803012716	0.0809699910331	0.45788727596	-0.106650466693	-0.357995097459	0.384014189462	-0.0334982560746	-0.0340128008432	0.297351290837	-0.00141508552661	0.293108357388	14.7911493586	30.2082074714	123.636991547
34	2.36598604074	-0.769784937514	1.98200516537	1.11093603	-1.09261465801	3.53095619262	0.232803628758	0.0429863456907	-0.367164347779	-0.00825587672733	0.114038899127	0.133947420401	0.063816703413	-0.161322228261	-0.107197591419	0.346896156448	-0.0351978276926	0.0216928605803	0.245531805848	0.019621693679	0.270209284872	19.8088666781	36.2749058764	127.561279478
35	2.16372784708	-0.809441610149	2.48184323965	0.311596942827	-0.873631347978	2.90641033073	-0.232708710165	-0.00411881616506	0.275071166517	0.0481551417494	0.0652932282548	-0.00575138783654	-0.161876292822	-0.012412001843	0.0236293612025	0.281557449861	-0.0221075732333	-0.00546206110993	0.233989281695	0.0017928866222	0.253616793892	20.1784977394	41.3418911912	129.317007163
36	2.52207861061	-1.26008317454	1.65453413427	2.13005081795	-1.21710431651	3.56314314743	0.232760516755	0.228792699539	-0.0133530606234	-0.121918239905	-0.126422261462	0.194178848531	0.182184943947	-0.627360842356	-0.129991332091	0.24971052822	-0.0443326984536	-0.0338459529745	0.367512668847	0.0458278207477	0.28509160897	3.96978470281	39.1161072896	105.149069218
37	2.09635942445	-1.18027140101	2.12537098271	0.660894570637	-1.00627709341	3.16448704185	-0.121854727094	0.396631134309	-0.271811633979	-0.355675147788	-0.331166476852	-0.513984755244	0.986932689437	-0.206274517266	-0.176897975633	0.46042062026	-0.0338058393226	0.0184056887656	0.352314360346	-0.0120567518429	0.280349451107	10.2810781964	32.2297140103	103.169655095

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 17 )	A	A	-1 - 17	1 - 19
2	2	chain 'A' and (resid 18 through 35 )	A	A	18 - 35	20 - 37
3	3	chain 'A' and (resid 36 through 58 )	A	A	36 - 58	38 - 60
4	4	chain 'A' and (resid 59 through 99 )	A	A	59 - 99	61 - 101
5	5	chain 'A' and (resid 100 through 153 )	A	A	100 - 153	102 - 155
6	6	chain 'A' and (resid 154 through 177 )	A	A	154 - 177	156 - 179
7	7	chain 'A' and (resid 178 through 201 )	A	A	178 - 201	180 - 203
8	8	chain 'A' and (resid 202 through 223 )	A	A	202 - 223	204 - 225
9	9	chain 'A' and (resid 224 through 245 )	A	A	224 - 245	226 - 247
10	10	chain 'B' and (resid -2 through 17 )	B	E	-2 - 17	1 - 20
11	11	chain 'B' and (resid 18 through 35 )	B	E	18 - 35	21 - 38
12	12	chain 'B' and (resid 36 through 99 )	B	E	36 - 99	39 - 102
13	13	chain 'B' and (resid 100 through 137 )	B	E	100 - 137	103 - 140
14	14	chain 'B' and (resid 138 through 153 )	B	E	138 - 153	141 - 156
15	15	chain 'B' and (resid 154 through 201 )	B	E	154 - 201	157 - 204
16	16	chain 'B' and (resid 202 through 223 )	B	E	202 - 223	205 - 226
17	17	chain 'B' and (resid 224 through 237 )	B	E	224 - 237	227 - 240
18	18	chain 'B' and (resid 238 through 247 )	B	E	238 - 247	241 - 250
19	19	chain 'C' and (resid -2 through 17 )	C	G	-2 - 17	1 - 20
20	20	chain 'C' and (resid 18 through 35 )	C	G	18 - 35	21 - 38
21	21	chain 'C' and (resid 36 through 58 )	C	G	36 - 58	39 - 61
22	22	chain 'C' and (resid 59 through 137 )	C	G	59 - 137	62 - 140
23	23	chain 'C' and (resid 138 through 153 )	C	G	138 - 153	141 - 156
24	24	chain 'C' and (resid 154 through 201 )	C	G	154 - 201	157 - 204
25	25	chain 'C' and (resid 202 through 223 )	C	G	202 - 223	205 - 226
26	26	chain 'C' and (resid 224 through 245 )	C	G	224 - 245	227 - 248
27	27	chain 'D' and (resid -2 through 17 )	D	J	-2 - 17	1 - 20
28	28	chain 'D' and (resid 18 through 35 )	D	J	18 - 35	21 - 38
29	29	chain 'D' and (resid 36 through 68 )	D	J	36 - 68	39 - 71
30	30	chain 'D' and (resid 69 through 79 )	D	J	69 - 79	72 - 82
31	31	chain 'D' and (resid 80 through 99 )	D	J	80 - 99	83 - 102
32	32	chain 'D' and (resid 100 through 137 )	D	J	100 - 137	103 - 140
33	33	chain 'D' and (resid 138 through 153 )	D	J	138 - 153	141 - 156
34	34	chain 'D' and (resid 154 through 177 )	D	J	154 - 177	157 - 180
35	35	chain 'D' and (resid 178 through 201 )	D	J	178 - 201	181 - 204
36	36	chain 'D' and (resid 202 through 223 )	D	J	202 - 223	205 - 226
37	37	chain 'D' and (resid 224 through 246 )	D	J	224 - 246	227 - 249

-
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