PDB-7loo: S-adenosyl methionine transferase cocrystallized with ATP

ID or keywords:

Entry

Database: PDB / ID: 7loo

Title

S-adenosyl methionine transferase cocrystallized with ATP

Components

S-adenosylmethionine synthase

Keywords

TRANSFERASE / S-adenosyl methionine transferase

Function / homology

Function and homology information

methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli 908573 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Jackson, C.J. / Tan, L.L. / Laurino, P.

Citation

Journal: Jacs Au / Year: 2021
Title: Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases.
Authors: Gade, M. / Tan, L.L. / Damry, A.M. / Sandhu, M. / Brock, J.S. / Delaney, A. / Villar-Briones, A. / Jackson, C.J. / Laurino, P.

History

Deposition	Feb 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 18, 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	7loo.cif.gz	740.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7loo.ent.gz	512.4 KB	Display	PDB format
PDBx/mmJSON format	7loo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7loo_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	7loo_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7loo_validation.xml.gz	63.2 KB	Display
Data in CIF	7loo_validation.cif.gz	87.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lo/7loo ftp://data.pdbj.org/pub/pdb/validation_reports/lo/7loo	HTTPS FTP

-
Related structure data

Related structure data	7ll3C 7lnhC 7lnnC 7lo2C 7lowC 7lozC 1p7lS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1p7l-d 7loz-1 1fug-1 5a1g-1 1xra-2 1mxc-2 6fbp-1 4x05-d 7b7z-d 1rg9-d Search similar-shape structures by Omokage search (details) 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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: S-adenosylmethionine synthase

B: S-adenosylmethionine synthase

Q: S-adenosylmethionine synthase

R: S-adenosylmethionine synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.922, 117.780, 113.210
Angle α, β, γ (deg.)	90.000, 107.519, 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

-
Protein , 1 types, 4 molecules ABQR

#1: Protein	S-adenosylmethionine synthase / AdoMet synthase / MAT / Methionine adenosyltransferase Mass: 41998.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli 908573 (bacteria) / Gene: metK, HMPREF1611_00479 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZE41, methionine adenosyltransferase

#1: Protein

S-adenosylmethionine synthase / AdoMet synthase / MAT / Methionine adenosyltransferase

Mass: 41998.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli 908573 (bacteria) / Gene: metK, HMPREF1611_00479 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V0ZE41, methionine adenosyltransferase

-
Non-polymers , 7 types, 670 molecules

#2: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₂O₇P₂
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#7: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.61 Å³/Da / Density % sol: 52.87 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris 6.5, 15% ethylene glycol, PEG 3350 20%

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.95→39.79 Å / Num. obs: 123360 / % possible obs: 99.9 % / Redundancy: 7 % / B_iso Wilson estimate: 30.92 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.151 / Net I/σ(I): 8.2
Reflection shell	Resolution: 1.95→1.98 Å / Num. unique obs: 6027 / CC_1/2: 0.445

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1P7L

1p7l

Resolution: 1.95→35.99 Å / SU ML: 0.2298 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2066	6216	5.04 %
R_work	0.1702	117084	-
obs	0.172	123300	99.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 61.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→35.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11623	0	266	635	12524

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0067	12186
X-RAY DIFFRACTION	f_angle_d	0.8814	16553
X-RAY DIFFRACTION	f_chiral_restr	0.0568	1848
X-RAY DIFFRACTION	f_plane_restr	0.0055	2145
X-RAY DIFFRACTION	f_dihedral_angle_d	23.2486	4408

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 (%)
1.95-1.97	0.3686	211	0.3256	3832	X-RAY DIFFRACTION	99.63
1.97-2	0.3067	234	0.3049	3915	X-RAY DIFFRACTION	99.78
2-2.02	0.2987	197	0.2978	3840	X-RAY DIFFRACTION	99.95
2.02-2.05	0.3088	201	0.274	3893	X-RAY DIFFRACTION	99.88
2.05-2.07	0.299	217	0.2727	3859	X-RAY DIFFRACTION	99.9
2.07-2.1	0.268	216	0.2595	3891	X-RAY DIFFRACTION	100
2.1-2.13	0.3053	199	0.2541	3932	X-RAY DIFFRACTION	99.88
2.13-2.16	0.2927	172	0.2369	3918	X-RAY DIFFRACTION	99.95
2.16-2.2	0.2306	203	0.2256	3931	X-RAY DIFFRACTION	99.98
2.2-2.23	0.2359	217	0.2157	3844	X-RAY DIFFRACTION	99.98
2.23-2.27	0.2122	173	0.2008	3957	X-RAY DIFFRACTION	99.95
2.27-2.31	0.2338	171	0.1983	3926	X-RAY DIFFRACTION	99.98
2.31-2.36	0.2111	181	0.1864	3911	X-RAY DIFFRACTION	100
2.36-2.4	0.2097	218	0.181	3904	X-RAY DIFFRACTION	99.98
2.4-2.46	0.2206	227	0.1753	3866	X-RAY DIFFRACTION	99.98
2.46-2.51	0.2094	245	0.1758	3916	X-RAY DIFFRACTION	99.98
2.51-2.58	0.2222	178	0.168	3867	X-RAY DIFFRACTION	99.98
2.58-2.65	0.1914	209	0.1658	3902	X-RAY DIFFRACTION	99.98
2.65-2.72	0.1889	247	0.1527	3900	X-RAY DIFFRACTION	99.95
2.72-2.81	0.1887	245	0.1509	3854	X-RAY DIFFRACTION	99.95
2.81-2.91	0.1789	210	0.1508	3884	X-RAY DIFFRACTION	99.95
2.91-3.03	0.2019	211	0.1608	3896	X-RAY DIFFRACTION	100
3.03-3.17	0.2061	212	0.1574	3880	X-RAY DIFFRACTION	99.8
3.17-3.33	0.187	229	0.16	3908	X-RAY DIFFRACTION	99.83
3.33-3.54	0.1967	200	0.1468	3923	X-RAY DIFFRACTION	99.71
3.54-3.82	0.171	196	0.1439	3925	X-RAY DIFFRACTION	99.98
3.82-4.2	0.1986	204	0.1407	3931	X-RAY DIFFRACTION	99.95
4.2-4.81	0.1615	168	0.1305	3971	X-RAY DIFFRACTION	99.93
4.81-6.05	0.1951	218	0.1513	3921	X-RAY DIFFRACTION	99.81
6.05-35.99	0.1953	207	0.1647	3987	X-RAY DIFFRACTION	99.34

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	1.37450697031	-0.346190211054	-0.0433948585027	1.64750557711	-0.0720691236498	0.427315637165	0.080465403555	0.0568486994505	0.133332321102	-0.142354005413	-0.0973053714335	-0.221034846042	-0.0329099517649	0.0845383081258	0.0169989254172	0.158654040644	-0.00369631227159	0.00875318428004	0.199182947963	0.0150714100369	0.307213722487	10.2920628183	3.7377950698	48.9978893736
2	3.01422374976	-0.927796824161	-0.894695392705	3.13963192806	0.75573951892	3.03409545243	-0.129066728629	-0.41633050132	-0.310704364911	0.351537048935	0.108783278116	-0.254000746861	0.196432745018	0.167969496351	0.0210033595454	0.172895134574	0.0278075874636	-0.0569490966999	0.245803972032	0.100649723189	0.395180809218	14.8772277867	-19.4133839021	61.6370677632
3	1.35120632767	-0.494993972083	-0.229659374373	2.45646971835	0.155036686695	0.201444796033	-0.0490654976563	-0.309461066359	0.0558410786077	0.31369105336	0.0712778142569	-0.115623079706	0.00277040993444	0.0612905685075	-0.0249498977071	0.193218564068	-0.00433456222924	-0.0362826153108	0.252951913918	-0.0103974834045	0.277225021446	6.78646139462	3.12102806583	64.0158155848
4	1.9478011606	0.195525873472	0.189054309371	4.45597528145	0.764676874681	2.4325449664	0.044228076151	-0.501573177428	0.367830728309	0.722205145107	0.0409086267586	-0.517940918654	-0.117658897684	0.31158767459	-0.0715780520705	0.286576475913	-0.0500294487448	-0.107698653385	0.378652352798	-0.0609785037863	0.565060343591	15.8651007559	12.0336414701	67.4996447343
5	1.24398748569	-1.19974142042	1.56795890738	1.37229374013	-0.464822112489	5.41978083163	0.0183580079672	1.1288975705	0.418011021428	-0.850473983652	-0.0395835059172	0.0314394279026	-0.742466049481	-0.0554807640538	0.120447184176	0.953000048378	0.211409311517	0.124582724636	0.825629397353	0.16750263875	0.364920092148	-0.469369120822	11.059675917	12.9651782788
6	8.62092372216	-0.0874202969378	-2.3741398377	3.35864432242	-0.0211689371458	4.52328303288	0.208435374698	0.525861739877	0.260146009431	-0.575057370614	-0.105722790945	-0.241542704303	-0.263443723874	0.446097622612	-0.101974176924	0.576485260967	0.052395823544	0.0478832710808	0.498197313372	0.090653363024	0.245984477663	5.01662018869	9.44007324175	25.2586627274
7	0.572902852998	-0.075980518234	0.957658969352	1.50256585181	-0.324892051975	2.52311035749	0.298590150698	1.10950104279	0.294011499841	-0.849021960124	-0.244051774235	-0.036531778374	-0.653448639017	-0.33137979364	0.017203254297	1.32796228205	0.358158067831	0.0201163085517	1.202224552	0.255845327303	0.499052864778	-5.91853819587	12.9035603274	4.41466085364
8	0.902945218431	1.26906662707	-1.85231992478	2.47420675525	-1.68965686125	5.33579613408	-0.0833915643058	1.3502790771	0.560922029572	-1.0630341506	-0.361117844394	0.565745432753	-0.279317355123	-0.659362252146	0.340835203731	1.48859983181	0.533953103705	-0.267962280661	1.51016927098	0.19807069837	0.799225015747	-21.5332390388	19.0255493604	1.53292130468
9	0.3804144286	0.821175197433	0.138537300491	1.79275505529	0.50777882607	3.13714758426	0.0942532273316	0.901867018222	0.0768166920335	-0.710339628558	-0.13173521129	0.264073740256	-0.13095063092	-0.191914141915	0.0436839175579	0.881274602555	0.21822708022	-0.0453473165005	0.919465639449	0.115745748807	0.413545754774	-5.95860238697	6.06937420632	10.2728346712
10	0.295746078261	0.345953657818	-0.486125797661	1.55876026639	-0.718408430885	0.810026211872	0.0406195813296	1.26521464633	0.195640410446	-0.752855850703	0.0271400072904	0.194548000111	0.219588325476	-0.496190164631	-0.0889996372025	1.54941724678	0.485011303018	0.428276725313	1.69997430606	0.337688931029	0.102519976286	10.0515738327	8.88011431081	-4.28490719959
11	0.27662875038	0.712276207032	-0.754862692249	1.96894297432	-2.17456985685	2.61732883604	0.302297352905	0.674856636709	-0.410202619872	-0.996124236384	-0.239397515935	-0.540456857664	-0.0664498861812	0.760726039588	0.162907918573	1.37353570028	0.250374301815	0.369053188578	1.64624301781	0.176655856076	0.634064228463	17.4439219986	6.11823844395	-6.71109929224
12	1.6101756555	1.08966996289	-0.665882318298	0.754342054678	-0.694886892796	2.10119847912	-0.0611288961675	0.829192008668	0.406760165668	-1.04918947963	-0.266792463668	-0.360179221897	-1.08470455074	0.523498896906	0.0109261470066	1.56844636559	0.219222996966	0.372688001915	1.31260175476	0.421946952037	0.590344565939	9.85930487981	17.78625568	1.6444983437
13	1.57710535261	-0.21397088923	0.291932629896	2.28129229488	0.589195605051	1.37620666835	0.118850689259	0.0793405977627	-0.150460487882	-0.233913842228	-0.136624752519	0.220816558578	0.0339961878449	-0.135139239514	0.0284848026	0.168383259668	0.0182267185574	-0.0280778823463	0.214575351989	0.00767970152187	0.341532501935	-10.3541789708	-3.57082201635	47.672150854
14	1.15818245628	-0.158825696483	0.0786337544074	1.52860038695	0.0451158422256	0.770692169934	0.0510690290217	0.0458616042324	-0.143206568508	-0.092821292488	-0.0483716600101	0.250632546103	0.00385432877821	-0.117705829597	-0.019809821392	0.14359227722	-0.0116624543437	-0.0106188889228	0.211367498178	-0.016553556675	0.31841153921	-10.3799156946	-6.08181431567	50.0537990975
15	3.25343643169	-0.971608673414	0.781460105492	3.10242013586	-0.887524044417	3.24978812279	-0.144580934393	-0.414589083467	0.317304188051	0.396545538115	0.0948805885769	0.305435188362	-0.216059600924	-0.203013974999	0.0456738928084	0.181412208467	0.027450342126	0.0569455661482	0.235037239482	-0.0921838986536	0.380165275784	-15.036335748	18.1617769074	61.6123851546
16	1.17316968084	-0.267654527564	0.111279410714	2.7437753681	-0.311062040831	0.264555540014	-0.033821788469	-0.199760923282	0.0315062532508	0.228404125666	0.0564998715679	0.157642617791	-0.00902749322879	-0.0776467371265	-0.0404495285221	0.170423954553	-0.00610703989661	0.0289121187405	0.22713717263	-0.0016914741007	0.277880979194	-7.69788324014	-1.78337024934	61.5500754381
17	2.13358639292	-0.241333101056	-1.12640564289	4.77546938621	2.66795584457	5.62270765404	0.0455817342378	-0.850638432901	-0.389529166728	0.970021870559	0.105681048775	0.0790069235415	0.179191069813	-0.249358062816	0.0196552306819	0.371500697217	0.0526258809596	0.0296884926252	0.528765427929	0.117333379303	0.250242776646	-4.19460307926	-13.925424518	74.4654893307
18	2.27694672906	0.129142120921	-0.126278763903	4.5831596642	-0.955451040829	2.64384634217	0.0512149944256	-0.473564466171	-0.334109770275	0.664646274565	0.0843479542444	0.54723602761	0.0971626413509	-0.288755832326	-0.119503832519	0.256255980246	-0.036928589555	0.0913791725476	0.352114768911	0.0656018982696	0.537340750251	-16.1678253053	-13.0401302168	67.1830491701
19	2.21617471138	-1.38627356977	-2.26220485373	1.34579092148	0.224380210359	5.01323280321	0.0867907920675	1.13766939325	-0.280182570369	-0.875061715339	-0.0800024182217	0.0919357830801	0.778080518106	0.00120012838246	0.163256277804	0.982097202533	0.229262088753	-0.113483340842	0.867748978315	-0.196218933004	0.355558802162	0.439837034837	-12.2675526855	12.9632667629
20	8.07522483892	0.429425648751	1.80977704264	3.00105455301	0.259480953173	3.64461238681	0.174723827807	0.733100021267	-0.197793794483	-0.564212559576	-0.125462766724	0.216960390336	0.26969870486	-0.27936896519	-0.0534506727223	0.599683877174	0.0471511167086	-0.0742651781857	0.483656680089	-0.106075194537	0.270948287473	-5.05447039688	-10.670603167	25.2584272382
21	0.190798428382	0.0751396579852	-0.339895515071	1.28844438187	0.12528452108	3.13428915945	0.210737667139	0.997189105966	-0.259719390067	-0.825967899605	-0.192703749497	0.00824735547675	0.536475459626	0.308841168436	0.0288944376294	1.28706770287	0.29915649612	0.000450971784284	1.16188590509	-0.192890860185	0.514924567001	6.06662727665	-14.2100993514	4.66534195155
22	0.316532412492	0.506276790439	-0.14998527087	1.17670151818	-0.381578880103	1.84925415919	0.371623552016	1.16820412554	-0.127010106384	-1.10391968194	-0.357584031578	-0.358050300912	0.196746299652	0.163684872179	-0.000316789144903	1.25169849316	0.423157118532	-0.0034979036826	1.29178005131	-0.242443538131	0.378863989645	5.23410022148	-11.3732062936	3.90229486509
23	1.66568250558	1.25120794775	-0.227177175285	1.75003120136	1.64568004587	4.85422958672	-0.129156839302	1.39596094986	-0.203647201043	-1.01139226202	-0.276887947485	0.2982524944	0.0196601676113	-0.503273945595	0.499391393971	1.41793260356	0.2066421715	-0.170504232533	1.53360187655	-0.135143947549	0.595176303048	-13.5620674241	-3.33858518801	-8.49355455055
24	2.18253593102	1.54845114463	0.310054626181	1.48848414086	1.59077455354	4.95797475227	0.141631853583	0.876002728253	0.0136147303751	-0.781046122946	-0.122094788402	0.440205713115	0.998290271405	-0.851186850085	-0.0269106433057	1.37108502497	0.089329215132	-0.296080250502	1.30069528104	-0.250688480614	0.628001372549	-13.931049069	-15.5082384073	-0.887874077821

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 135 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 136 through 224 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 225 through 321 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 322 through 381 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 33 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 34 through 106 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 107 through 194 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 195 through 220 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 221 through 269 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 270 through 300 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 301 through 344 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 345 through 380 )
13	X-RAY DIFFRACTION	13	chain 'Q' and (resid 3 through 63 )
14	X-RAY DIFFRACTION	14	chain 'Q' and (resid 64 through 135 )
15	X-RAY DIFFRACTION	15	chain 'Q' and (resid 136 through 224 )
16	X-RAY DIFFRACTION	16	chain 'Q' and (resid 225 through 300 )
17	X-RAY DIFFRACTION	17	chain 'Q' and (resid 301 through 321 )
18	X-RAY DIFFRACTION	18	chain 'Q' and (resid 322 through 380 )
19	X-RAY DIFFRACTION	19	chain 'R' and (resid 3 through 33 )
20	X-RAY DIFFRACTION	20	chain 'R' and (resid 34 through 106 )
21	X-RAY DIFFRACTION	21	chain 'R' and (resid 107 through 194 )
22	X-RAY DIFFRACTION	22	chain 'R' and (resid 195 through 300 )
23	X-RAY DIFFRACTION	23	chain 'R' and (resid 301 through 321 )
24	X-RAY DIFFRACTION	24	chain 'R' and (resid 322 through 379 )

-
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://pdbjlvh1.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, 4 molecules ABQR

-
Non-polymers , 7 types, 670 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, 4 molecules ABQR

-Non-polymers , 7 types, 670 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, 4 molecules ABQR

-
Non-polymers , 7 types, 670 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