[English] 日本語

Yorodumi

- PDB-8ukz: Structure of P450Blt from Micromonospora sp. MW-13 with E238A Mutation -

+
Open data

-
Basic information

Entry

Database: PDB / ID: 8ukz

Title

Structure of P450Blt from Micromonospora sp. MW-13 with E238A Mutation

Components

Cytochrome P450-SU1

Keywords

OXIDOREDUCTASE / mutant / biarylitide / crosslink

Function / homology

Function and homology information

Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function

Biological species

Micromonospora sp. MW-13 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Hansen, M.H. / Cryle, M.J.

Funding support

Australia, 2items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Structural Insights into a Side Chain Cross-Linking Biarylitide P450 from RiPP Biosynthesis
Authors: Hansen, M.H. / Keto, A. / Treisman, M. / Sasi, V.M. / Coe, L. / Zhao, Y. / Padva, L. / Hess, C. / Leichthammer, V. / Machell, D.L. / Schittenhelm, R.B. / Jackson, C.J. / Tailhades, J. / ...

History

Deposition	Oct 15, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 10, 2024	Provider: repository / Type: Initial release

-
Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Downloads & links

-
Download

PDBx/mmCIF format	8ukz.cif.gz	715 KB	Display	PDBx/mmCIF format
PDB format	pdb8ukz.ent.gz	542.5 KB	Display	PDB format
PDBx/mmJSON format	8ukz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ukz_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8ukz_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8ukz_validation.xml.gz	41.2 KB	Display
Data in CIF	8ukz_validation.cif.gz	57.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uk/8ukz ftp://data.pdbj.org/pub/pdb/validation_reports/uk/8ukz	HTTPS FTP

-
Related structure data

Related structure data	8u2mC 8u3nC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#82 - Oct 2006 Cytochrome p450 similarity (1)

-
Assembly

Deposited unit

A: Cytochrome P450-SU1

B: Cytochrome P450-SU1

C: Cytochrome P450-SU1

hetero molecules

138 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: Cytochrome P450-SU1

hetero molecules

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

B: Cytochrome P450-SU1

hetero molecules

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

C: Cytochrome P450-SU1

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.957, 94.480, 105.985
Angle α, β, γ (deg.)	90.000, 92.680, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 14 through 32 or resid 34...
d_2	ens_1	(chain "B" and (resid 14 through 32 or resid 34...
d_3	ens_1	(chain "C" and (resid 14 through 32 or resid 34...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	TYR	TYR	LEU	LEU	A	A	14 - 32	35 - 53
d_1	2	GLU	GLU	VAL	VAL	A	A	34 - 38	55 - 59
d_1	3	TRP	TRP	CYS	CYS	A	A	40 - 55	61 - 76
d_1	4	GLN	GLN	VAL	VAL	A	A	57 - 110	78 - 131
d_1	5	GLN	GLN	GLU	GLU	A	A	112 - 124	133 - 145
d_1	6	GLY	GLY	VAL	VAL	A	A	130 - 169	151 - 190
d_1	7	SER	SER	GLU	GLU	A	A	171 - 204	192 - 225
d_1	8	GLY	GLY	ALA	ALA	A	A	206 - 215	227 - 236
d_1	9	ASP	ASP	VAL	VAL	A	A	265 - 289	286 - 310
d_1	10	ASP	ASP	LEU	LEU	A	A	291 - 354	312 - 375
d_1	11	GLU	GLU	ALA	ALA	A	A	356 - 363	377 - 384
d_1	12	LEU	LEU	SER	SER	A	A	368 - 391	389 - 412
d_2	1	TYR	TYR	LEU	LEU	B	B	14 - 32	35 - 53
d_2	2	GLU	GLU	VAL	VAL	B	B	34 - 38	55 - 59
d_2	3	TRP	TRP	CYS	CYS	B	B	40 - 55	61 - 76
d_2	4	GLN	GLN	VAL	VAL	B	B	57 - 110	78 - 131
d_2	5	GLN	GLN	GLU	GLU	B	B	112 - 124	133 - 145
d_2	6	GLY	GLY	VAL	VAL	B	B	130 - 169	151 - 190
d_2	7	SER	SER	GLU	GLU	B	B	171 - 204	192 - 225
d_2	8	GLY	GLY	ALA	ALA	B	B	206 - 215	227 - 236
d_2	9	ASP	ASP	ASP	ASP	B	B	219	240
d_2	10	ALA	ALA	VAL	VAL	B	B	266 - 289	287 - 310
d_2	11	ASP	ASP	LEU	LEU	B	B	291 - 354	312 - 375
d_2	12	GLU	GLU	ALA	ALA	B	B	356 - 363	377 - 384
d_2	13	LEU	LEU	SER	SER	B	B	368 - 391	389 - 412
d_3	1	TYR	TYR	LEU	LEU	C	C	14 - 32	35 - 53
d_3	2	GLU	GLU	VAL	VAL	C	C	34 - 38	55 - 59
d_3	3	TRP	TRP	CYS	CYS	C	C	40 - 55	61 - 76
d_3	4	GLN	GLN	VAL	VAL	C	C	57 - 110	78 - 131
d_3	5	GLN	GLN	VAL	VAL	C	C	112 - 169	133 - 190
d_3	6	SER	SER	GLU	GLU	C	C	171 - 204	192 - 225
d_3	7	GLY	GLY	ALA	ALA	C	C	206 - 215	227 - 236
d_3	8	ASP	ASP	ASP	ASP	C	C	219	240
d_3	9	ALA	ALA	VAL	VAL	C	C	266 - 289	287 - 310
d_3	10	ASP	ASP	LEU	LEU	C	C	291 - 354	312 - 375
d_3	11	GLU	GLU	SER	SER	C	C	356 - 391	377 - 412

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.560235408689, -0.822783302774, 0.0957283841247), (-0.82474944631, -0.564812804572, -0.0278360665867), (0.076971667917, -0.0633571816625, -0.995018205798)	-49.6424893263, -84.3299250137, -70.6423880528
2	given	(0.488779971403, 0.870846511858, 0.0521583391124), (0.871331655082, -0.490271869634, 0.0203627281292), (0.0433045771968, 0.0354943182725, -0.99843120292)	-26.9871823014, -60.2503172697, -34.1962046526

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein	Cytochrome P450-SU1 Mass: 45274.238 Da / Num. of mol.: 3 / Mutation: E238A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora sp. MW-13 (bacteria) / Gene: C5N14_21030 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E2YLT4

-
Non-polymers , 5 types, 224 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-TFA / trifluoroacetic acid Mass: 114.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂HF₃O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.09 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 12% PEG400 and 14% PEG 20K

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95373 Å / Relative weight: 1
Reflection	Resolution: 1.95→47.24 Å / Num. obs: 88780 / % possible obs: 99.89 % / Redundancy: 3.5 % / B_iso Wilson estimate: 34.75 Å² / CC_1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 5.68
Reflection shell	Resolution: 1.95→2.02 Å / Num. unique obs: 8823 / CC_1/2: 0.257 / CC star: 0.64

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→47.24 Å / SU ML: 0.2519 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4687
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2228	4499	5.07 %
R_work	0.2046	84226	-
obs	0.2055	88725	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: 47.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→47.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8559	0	180	212	8951

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	8984
X-RAY DIFFRACTION	f_angle_d	0.6847	12303
X-RAY DIFFRACTION	f_chiral_restr	0.0416	1367
X-RAY DIFFRACTION	f_plane_restr	0.0059	1638
X-RAY DIFFRACTION	f_dihedral_angle_d	7.8349	1314

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	2.49880385567
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	2.49547799663

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	0.3068	155	0.3375	2775	X-RAY DIFFRACTION	99.36
1.97-2	0.3447	156	0.318	2797	X-RAY DIFFRACTION	99.8
2-2.02	0.3545	133	0.3151	2777	X-RAY DIFFRACTION	99.59
2.02-2.05	0.3367	140	0.3063	2786	X-RAY DIFFRACTION	99.73
2.05-2.07	0.3032	161	0.2914	2806	X-RAY DIFFRACTION	99.8
2.07-2.1	0.3163	141	0.2837	2777	X-RAY DIFFRACTION	99.76
2.1-2.13	0.2786	159	0.2667	2820	X-RAY DIFFRACTION	99.93
2.13-2.16	0.3167	125	0.2707	2786	X-RAY DIFFRACTION	99.73
2.16-2.2	0.2874	155	0.256	2809	X-RAY DIFFRACTION	100
2.2-2.23	0.288	154	0.2556	2776	X-RAY DIFFRACTION	99.9
2.23-2.27	0.2613	140	0.2389	2815	X-RAY DIFFRACTION	99.93
2.27-2.31	0.2803	141	0.2297	2837	X-RAY DIFFRACTION	99.97
2.31-2.36	0.2441	151	0.2211	2797	X-RAY DIFFRACTION	99.93
2.36-2.41	0.245	154	0.2178	2804	X-RAY DIFFRACTION	100
2.41-2.46	0.2432	152	0.2143	2795	X-RAY DIFFRACTION	100
2.46-2.51	0.253	140	0.2061	2799	X-RAY DIFFRACTION	100
2.51-2.58	0.2216	166	0.2025	2809	X-RAY DIFFRACTION	100
2.58-2.65	0.2413	144	0.2032	2778	X-RAY DIFFRACTION	100
2.65-2.72	0.247	180	0.2062	2796	X-RAY DIFFRACTION	100
2.72-2.81	0.2593	142	0.2094	2805	X-RAY DIFFRACTION	100
2.81-2.91	0.2095	135	0.2052	2820	X-RAY DIFFRACTION	99.97
2.91-3.03	0.2603	140	0.2115	2823	X-RAY DIFFRACTION	99.97
3.03-3.17	0.2653	151	0.2224	2792	X-RAY DIFFRACTION	100
3.17-3.33	0.2073	168	0.2046	2825	X-RAY DIFFRACTION	100
3.33-3.54	0.2008	159	0.1929	2820	X-RAY DIFFRACTION	100
3.54-3.82	0.2043	139	0.1811	2819	X-RAY DIFFRACTION	100
3.82-4.2	0.1896	148	0.1686	2834	X-RAY DIFFRACTION	99.93
4.2-4.81	0.1742	158	0.1594	2817	X-RAY DIFFRACTION	100
4.81-6.06	0.1943	127	0.195	2864	X-RAY DIFFRACTION	99.9
6.06-47.24	0.1835	185	0.1837	2868	X-RAY DIFFRACTION	99.87

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	2.03987635595	-0.261872014648	1.48391118543	2.03697491416	0.117016226546	9.63797083549	0.319466704556	-0.0483235441592	0.300130576072	-0.296455448906	-0.280572424316	0.342786828362	-1.63331663003	-2.20488572612	-0.11466875904	0.738897381158	0.188679015529	-0.0605504362723	0.624945351614	-0.0132997311319	0.453646189084	-51.818	-26.612	-25.024
2	9.37586677565	4.99124948835	0.927599346309	4.672277449	4.85931494594	9.54473167255	-0.70904350824	-0.0325097357148	0.144598051181	-0.185081305151	-0.337635782005	2.54196353787	0.620942196788	-1.91394565002	0.917722479096	0.431855875813	-0.174669891932	0.0301623774106	0.947944865676	0.00931877006683	0.541477130481	-50.371	-34.192	-25.086
3	2.06007018443	-1.02627590324	-2.07858183888	5.30673225794	-0.374973118972	3.66387957486	0.0015944305946	-0.776704378206	-0.414511053217	0.352462386105	0.241527441707	0.914940083792	0.997436661197	-0.439465914787	-0.322121997612	0.448611980559	-0.0097021220486	0.0147237921435	0.406647909494	0.145583692481	0.381739165563	-40.635	-35.79	-18.696
4	1.65039314703	-0.285748801874	-0.100923767787	1.69096365984	-0.462820590618	2.14862407102	-0.0171186396695	-0.0148778168056	0.0520425156859	-0.0672489313856	-0.0337556570479	-0.199944086291	0.158981136279	0.200060501591	0.0389104772884	0.185568102005	-0.00202818282313	-0.00246965343657	0.215559934609	-0.0030933040958	0.220389056774	-21.857	-21.214	-31.991
5	2.91821173122	3.97446256342	-3.62493980225	5.37867962385	-4.92956764767	4.53443330359	-0.11599867398	0.39451832526	0.2287509072	-0.887147140802	-0.0106879133129	-0.0720273761213	0.267795757531	-0.289296463012	0.120117269336	0.443846392537	0.0684867118164	-0.0138252260004	0.283221988809	0.000215655977775	0.25076820499	-24.351	-24.288	-38.703
6	2.29000874738	-1.90639563653	1.98974518268	2.10483271868	-1.88831012646	4.14843057167	0.0114514095127	-0.0304075901773	0.152160734817	-0.347874414997	-0.0113897197524	-0.290640250938	0.136903461715	-0.142050920755	-0.0460250320383	0.169904110745	0.00929170927398	0.0360880778492	0.21995565899	0.00302485305934	0.290819668138	-34.363	-17.807	-34.068
7	5.54331689734	-4.57319909033	2.13620123492	3.52440618037	-2.28438505811	3.93997768268	-0.0496989684456	0.233079261183	0.747457100768	0.266136075807	-0.312647202208	-0.689831039886	-0.525033837711	0.333052124485	0.315970313105	0.339693922986	-0.0446734970269	0.0299469205154	0.28859356067	-0.039175305873	0.345628603159	-24.378	-6.787	-21.787
8	2.44976176264	-1.87112421212	-0.569104129187	2.27062246171	0.273433853918	2.47687769304	-0.0256742833368	-0.0208753647223	0.15242483421	-0.514756505814	-0.167008662631	0.64779979119	0.0568722234666	-0.102314157678	0.0476305756256	0.232431713372	0.00767384018488	-0.0676723970823	0.317579087978	-0.043262915117	0.290622398986	-32.566	-19.475	-27.093
9	1.63591951808	1.05722273036	-0.642910060038	3.39080235843	-3.19692236569	3.11201037101	-0.00696260933646	0.245523498514	-0.254007601481	-0.130678555972	0.274095631863	-0.0766295609883	0.461745119824	0.0116926302177	-0.29667313599	0.360936234709	0.0118148490858	0.056296325828	0.247183191021	-0.0818245070713	0.384336690305	-44.207	-64.263	-49.941
10	2.01820736348	1.46673031849	-2.8880586109	1.86719494456	-1.65367818728	8.75980053756	-0.170478145691	0.052344650929	-0.569965252933	-0.515942910943	-0.13281847962	-0.0152920432177	0.636065447747	0.230049106676	0.334591134652	0.386687097511	0.140581011428	-0.0731130325353	0.327102163542	-0.0492451557062	0.456008419646	-32.803	-60.259	-43.991
11	6.14789316979	2.70743591587	-1.20560894606	4.15492761177	-4.30854249266	4.70065830056	0.161955797202	0.107682417724	0.0428479749631	0.155614569301	-0.142277983353	-0.321054687297	-0.133307844249	0.724427274092	-0.0188315937487	0.332688158104	-0.0240586138046	0.0268922698792	0.346751414288	-0.123170616761	0.367297314754	-30.495	-42.179	-44.267
12	3.71347476789	-0.254537568064	-3.14186240647	7.25015127539	-3.11982167565	4.22838045717	0.127508126138	1.43452457191	0.525690814818	-0.889929745163	0.241836566171	-0.0468810764645	0.0545545442555	0.655052748179	-0.376003362858	0.525322505383	-0.0952825711895	0.0942880051757	0.62356576527	0.0358659308806	0.349221510544	-35.644	-32.521	-56.876
13	5.03451995678	-3.95368734912	-0.401037994669	6.46146024833	3.56957684996	3.17147899547	-0.125734572357	-0.0730052927456	0.120727792487	0.125295832703	0.235233290678	-0.266974709647	0.104853166569	0.180694209135	-0.0950321293091	0.363407157769	-0.0280070275758	-0.0423640505827	0.229925813558	0.0130307696259	0.323477996542	-42.598	-32.042	-42.823
14	3.22781101295	1.36942272182	2.05536066844	3.22659421656	5.25877353951	8.34369444621	-0.00704694345811	-0.049054280184	0.239425359322	-0.0393514797156	0.076224411801	0.102217114757	-0.517990945567	-0.112234864474	-0.0626380330934	0.328705742059	0.108321055725	0.0305380289566	0.350154656027	0.0504316773524	0.461138566355	-67.177	-39.301	-42.551
15	5.23749694727	7.58836956231	0.988032942479	2.00514354527	2.5936841159	8.31877448719	-0.580807191773	0.733602147681	-0.00666556146173	-0.268245570372	0.553336352156	-0.0698666191505	-0.319512285874	-0.808469725547	0.0194613210287	0.499383379821	0.14321744871	-0.0289974697263	0.560285219246	-0.0156738678696	0.492867044599	-76.382	-55.024	-51.78
16	1.79261550568	-0.790821419149	0.371694408533	4.42551997642	0.277922421727	4.19823434708	0.115221765366	0.114805621707	0.00973827173409	-0.597053400464	-0.0645880247306	0.497906406574	-0.117006333705	-0.393222622303	-0.0602573046362	0.219735946993	0.0339907164617	-0.0466145188412	0.232340561434	0.0107312666832	0.309375748554	-63.252	-45.345	-53.453
17	9.50471742678	-7.14696763491	0.374862384246	9.16419440169	-0.181912781343	5.60257368894	0.181318187034	0.658727816188	-0.0971527223746	-0.721803047301	-0.0402408602172	0.0554035866037	-0.286001823023	0.179635855407	-0.151257511046	0.345877724042	-0.0375710703061	0.0157322500384	0.228033909961	-0.030316692004	0.269561046736	-45.784	-47.436	-61.561
18	7.0841260019	-1.17674408205	1.70080568291	6.46610006211	-2.05039511663	9.28765901954	-0.00058545534893	0.323141909864	0.598778630223	-0.559058328353	-0.0427901856394	-0.0390696698364	-0.75837648172	-0.545730022735	0.00305106677044	0.359662287981	0.0102080394145	-0.0205916725481	0.190927679581	0.0337562590151	0.378154144092	-56.036	-28.466	-55
19	3.81749113624	4.59924957516	4.10381432975	6.8308382684	2.2207577336	9.92964996314	-0.169796734558	0.392792537915	1.40341811489	0.677029523805	0.1380756589	-0.0655957611291	-0.958099515559	0.18070469814	-0.032215765113	0.525283614045	0.0840236696402	-0.0397864656895	0.277229009018	0.00463463145609	0.537374202453	-49.994	-22.296	-46.143
20	9.75622920814	1.47263428075	1.92109665904	4.84274891126	-1.13957408265	6.34117046349	-0.188968545679	0.651693343281	0.478717238932	-0.467026180344	0.101975636855	0.277920996173	-0.387472329472	0.2759382634	0.100912784884	0.356235155944	0.0326757176629	-0.00857661430789	0.233845443239	0.0129908404674	0.288051589458	-45.533	-31.105	-52.076
21	2.25974060019	0.74032871022	-1.25110706402	0.826718395642	-1.43611726146	2.83928558837	0.00671453089429	-0.173879750021	0.034339013627	0.0517412431315	0.167568698844	0.137029419127	-0.125979811169	-0.215360885111	-0.172885393444	0.302656310321	0.0398173676604	0.0113272376887	0.205120919811	0.0160891695147	0.289119159594	-56.479	-52.839	-39.86
22	2.41952266795	-2.10980512873	0.471197632041	7.03300424614	-4.51121674718	3.44486175904	0.0470626492865	-0.107636485263	0.039998708668	0.377112198066	0.195804126305	-0.449350004327	0.14953799659	1.38143933275	-0.154737045263	0.290428149624	0.0243413823983	-0.0876533809418	0.58266028072	-0.105823871898	0.410087340626	-23.817	-49.09	-42.398
23	4.55952653642	1.19222905582	-3.41681799852	0.96896779946	-1.21534368051	5.04446614689	-0.260005502553	-0.21155942943	-0.32672913998	0.0619132022911	0.130266456188	-0.103998429043	0.63258781376	0.00132713752021	0.130226361433	0.337472781813	0.0302459047919	-0.0279602747067	0.216908597119	0.0070220902944	0.28442047861	-44.638	-58.34	-35.475
24	5.77706572003	5.34613157743	-6.20448096131	4.83895553008	-5.63372027064	6.46692332567	0.450468697133	-1.14203618195	0.485759341678	1.02809137438	-0.0841983766297	0.281545161979	-1.00184557458	0.383532269728	-0.460559112522	0.45150642143	0.0533134448273	0.026420677866	0.393488798661	-0.00994544315955	0.363346257919	-47.499	-51.567	-29.63
25	3.16339972511	3.60909342713	-0.898987554542	5.44059543331	-0.704426815894	2.18284225141	-0.0616316773013	0.0801200049621	0.464446315687	0.356433953684	0.183952894694	0.62578893468	-0.0681167840025	-0.241262101256	-0.15020393907	0.269087610618	0.0594335005993	0.0235651494975	0.210125528364	0.0104146698564	0.239203750757	-58.462	-46.795	-38.942
26	2.56633600811	2.37421100966	-1.27041050641	2.5762198096	-0.311613472406	2.08528709724	0.116794313542	0.120905920811	-0.292224566799	-0.153865452247	-0.0131922423945	0.104061269449	0.0628774269663	-0.161255443868	-0.0863869907618	0.285093580466	-0.0125998709297	-0.0393287868652	0.21756486412	-0.0140159261699	0.316285793058	-57.226	-59.667	-51.715
27	2.78280567726	1.01387329191	0.382245683357	1.74007465393	0.704362133184	1.49560855783	0.422159190411	-0.287817566689	0.482159887934	0.256956088608	-0.328509374622	0.525354621349	0.15404381041	-0.0710133344732	-0.0316409117477	0.340114695384	0.0381072744432	-0.0518298694573	0.238016960827	0.0358021957181	0.256278676818	-53.84	-49.81	-46.297
28	4.78303517394	-5.72126897098	-3.85279369222	8.75556698996	6.29397825393	7.75498537753	-0.374587024835	-0.275999324705	0.53014795209	0.0175364109313	0.396995977995	-0.297674361688	-0.869304999558	0.693134872081	-0.0304657037501	0.628473258229	-0.117409975865	-0.109921023398	0.386740241606	0.0424237156124	0.414396556594	-50.247	-59.1	-11.768
29	2.97792619996	-0.908262137379	1.14353052725	3.93148551852	1.40678215336	4.28019836709	-0.410451129282	-0.221153229808	0.287281180604	-0.113571648965	0.0378677746745	0.00150235143133	-0.496624777464	-0.60160251276	0.35607209894	0.516501354185	0.170960643401	-0.0440012274925	0.418474302071	-0.0576540647948	0.389633992844	-66.206	-56.734	-9.876
30	2.86969494375	1.48260165181	-0.0478012783429	2.18344619466	0.602015059798	0.458659480202	-0.0724389991115	-0.202805380812	0.300866211563	-0.501858412647	0.217148998677	0.977100656476	-0.158004801327	-0.438195340231	-0.254757467648	0.577705284504	0.0592648526399	-0.00333834193084	0.726938426981	0.0608514562359	0.477061023905	-79.971	-67.833	-15.367
31	2.48765857306	0.686121447326	-3.70472071423	2.16450148417	-2.38539223301	6.48343979308	0.0144656247381	-1.34386322496	0.121439592269	1.55076888277	0.182546214531	0.441700701675	0.636498840154	-1.02062090176	-0.194862856548	0.780555816652	0.00827828052479	0.0135744434779	0.750962443404	-0.0207912462255	0.459289171506	-77.827	-82.962	-5.365
32	7.02702709118	-1.38098235206	2.17350326392	3.10696759463	1.07779684864	6.33842776327	0.448959861466	-1.00474766492	-1.40533157921	1.68884394375	-0.129408156902	-0.381166119514	1.33550988158	-0.564181749215	-0.259878152758	1.05059281928	-0.175788732944	-0.288363528584	0.470658743747	0.199266435832	0.682597904232	-65.142	-93.225	-4.21
33	1.37123912815	0.738624576685	0.438875582763	3.7261725423	-1.74787633069	1.33292877252	0.546571508264	0.616397224323	-0.359555168351	-0.583021170892	0.0232641239314	0.303984601927	0.030928103513	-0.169008314268	-0.320579464724	1.05791871556	0.484977573209	-0.474120568681	-0.07016963669	-0.371336252272	1.47398548393	-50.433	-94.914	-11.269
34	5.55671841814	-5.1654769904	0.0815410866924	4.77923878702	-0.0377056530315	7.49905113842	-0.632323095171	-0.403969669429	-0.886723769315	-0.156279283327	0.226032009803	0.998892954714	0.212289480702	1.91396328343	0.347376370483	0.553405108124	0.23531675837	-0.000201396765117	0.616010167841	-0.0644509606422	0.579482562467	-41.814	-87.961	-16.166
35	2.1354138871	-0.138603939173	-0.0927600069823	4.68474691458	-1.34954592825	2.91699216534	0.097369722821	0.215606670262	-0.221468525883	-0.481802554422	0.142403424176	0.126518929431	0.573692892052	-0.164661042547	-0.270995390352	0.410249411845	-0.0541356852548	-0.0403756443947	0.340615093694	-0.0253958736086	0.293258208872	-60.701	-80.155	-21.557
36	9.99870626903	4.55232672081	-3.72952109721	6.5701835668	0.336653166512	2.39528154425	-0.329778785045	0.351028068315	-0.348797888319	-0.696873091658	0.567274899102	-0.15758971407	0.943874155237	-0.412135486275	-0.249115925531	0.570742586855	-0.148576033455	-0.147374652769	0.447304415089	0.0470109593721	0.426565819891	-74.762	-89.012	-20.365
37	4.08153501066	-2.92772830598	4.30415977549	9.13780692475	3.0029623612	9.81837470762	-0.019835697136	-1.12314531008	-1.15334223571	0.0601424264291	0.260466671663	0.843189196004	1.29853489921	-1.82300382044	-0.391828820975	0.72069533935	-0.350304638388	0.0123149049927	0.909473634535	0.0762742261097	0.630513410181	-82.585	-88.232	-12.831
38	2.4112605349	0.899949893848	1.42229293184	2.33472236402	0.97784728768	3.36571163202	-0.402723614148	0.0596077654756	0.185608323124	-0.134525664655	0.182179942089	0.319063102697	-0.0266420366911	-0.61280855329	0.219482393697	0.398491915469	-0.0567259522394	-0.0665074378549	0.481048845592	0.028133869268	0.336316695362	-69.001	-79.564	-14.446
39	9.37829233392	-1.42844877594	-1.99472073632	4.92079200694	-0.756135648946	2.21484282328	-0.28613365981	-0.230212082108	-0.524595758651	0.294130102162	0.258402480012	-0.010392092771	0.993475494837	-0.296597821308	0.042902648079	0.612592164013	0.0549271385994	-0.049185641153	0.553254068593	-0.0416317347647	0.393541491214	-48.349	-81.502	3.035
40	3.64825102268	-1.83607651221	2.00861277285	6.03991899326	-1.19120544563	2.73270126544	-0.188590163403	-0.229081082949	0.0197776426555	0.308093975062	0.205400322775	0.368135184886	-0.589261682938	-0.562025369347	-0.0460728658056	0.38324381465	0.108889107067	0.0196401048833	0.415108035676	0.012186800173	0.215306305828	-62.827	-65.584	-5.845
41	4.89267349917	3.62277602208	2.77861552354	4.08102691439	0.570684678471	3.08841240668	-0.284561258085	0.508616638812	1.37539512586	0.52208092773	0.0579054771976	0.202740834374	-1.07337389392	-0.37216905649	0.273354473135	1.28056453963	0.573510829243	0.00580821295525	0.761416801407	-0.104950975177	0.679811560189	-69.744	-48.856	-8.559
42	7.69172267644	-2.75351546312	2.8993072322	2.33307847762	-0.421457815671	2.36943741835	-0.0573098513639	-0.559463192084	0.27244996394	0.0437944388035	-0.0613387066451	-0.130434517658	-0.454365276406	-0.376290260347	0.0734984768868	0.430310677247	0.0504321344048	-0.0205785719472	0.35976604192	-0.0447871302772	0.228830758612	-57.233	-65.518	-0.128
43	9.24554354906	-5.06149470026	2.39734815874	2.95469445054	-2.40458926401	6.02209101317	0.209560855118	-0.437356551286	-0.237035606688	-0.399177553361	0.076856567916	-0.0353262103014	0.334116565649	-1.10771602717	-0.354387893626	0.384459898765	-0.0327675843969	-0.0293211939963	0.414624317203	0.060173660016	0.366910551632	-65.196	-79.107	-2.982
44	5.23841282692	-5.40179132196	5.02643701187	5.55806008904	-5.16213930357	4.80872802731	1.0699950921	-1.85784413471	-0.907349277717	-0.355809430403	-0.63003920766	-0.179367697497	1.26207184057	0.108409407826	-0.54793325364	0.636262495237	-0.123125095636	-0.135822514566	0.624380847144	0.0990742806661	0.685056054587	-50.197	-89.312	-0.339
45	9.02191508555	-7.08143842275	3.57419109664	8.56384365166	-2.46801765261	6.03274024972	-0.060178232576	0.177479117646	-0.0283740994872	-0.0769091692681	-0.0658062824362	-0.435343751509	0.145978065417	0.416695118884	0.109035133952	0.433842701424	-0.0462152217354	0.0266663200955	0.343069069191	-0.0241068706544	0.38201084238	-47.6	-75.496	-15.697
46	3.14107138687	0.598410920857	-2.72721686407	3.69612781379	4.2524769065	8.71936928399	0.846043071836	-0.985112202795	-0.953227240121	-1.06318810382	-0.0121624347238	-0.360179054447	0.319298310147	1.58843159455	-0.831647468482	0.365259456401	0.0876900036786	-0.0448373732426	0.717185632408	-0.146196748193	0.579048923162	-41.318	-84.232	-13.058
47	7.3255335138	3.3704241959	-5.05452916815	8.59536638517	-0.755959424076	7.06365285371	0.166150440114	-0.255070846538	0.659957985651	0.333783006346	-0.117125680961	-0.354732040128	-0.291086215831	0.575830895934	-0.102190838943	0.284346125078	-0.0238899939258	-0.0536546504258	0.348782554912	0.00750865223581	0.390957339201	-11.884	-16.98	-19.967
48	4.08138027993	-0.364802427467	-4.74252510396	3.701737271	4.05404420067	9.14837546577	0.367074734366	-0.499732057532	1.14689502628	-0.962530212181	0.506348777668	-0.541911792041	-0.646743181798	0.880544096991	-0.7250242975	0.365793438901	-0.0658604325873	0.0310617184438	0.439917217215	0.0432621907572	0.420696091477	-6.828	-22.073	-29.465
49	5.33413494006	-0.648519514749	-2.79565852649	5.84532901173	-4.19927025741	8.68418850095	0.0432331914493	-1.02721140567	0.191448128619	0.455994087941	-0.343968218444	-0.545940137752	-0.194565351698	1.4009359292	0.343941699455	0.296886601205	0.0732782124994	-0.0348719121261	0.565608744932	-0.0614346515297	0.470716000956	-9.009	-31.489	-23.337
50	3.91912034966	2.96414491062	-3.57807292336	4.41497345106	-1.392425343	3.80479491388	0.0543306188352	-0.0204943369383	-0.325900218525	-0.213770000684	-0.0013912769117	0.149220213544	0.404575129977	0.22893494617	-0.0616702759849	0.438984906516	0.0934142470722	-0.0573348778867	0.355876939749	0.0576933947011	0.385642669347	-21.154	-40.226	-27.11
51	6.09665825298	-1.9000932125	-0.413929843145	2.19515172235	-0.958643491017	7.38928287708	0.125879255703	-0.77242174767	-0.920974902924	0.235661084988	0.133642042895	0.0656225800582	1.08923943911	0.379542756375	-0.165489315654	0.52031119621	-0.000294549912238	-0.102485949543	0.329351199215	0.0605325444895	0.410731343132	-33.848	-40.589	-22.021
52	3.88131147303	-1.56357688541	0.173175554061	2.16938723242	1.33626642645	2.74923418417	-0.0736926568317	0.0905286623145	0.31014565771	0.0548703848637	0.0443469833278	0.21815660956	0.032306660008	-0.379611396495	0.00735971492809	0.208588352388	0.004102226306	-0.0013215995705	0.261956497548	-0.0132096958387	0.273220516595	-45.264	-20.552	-32.213
53	3.05979515082	3.10773165489	4.01181924828	4.64873220682	6.06131884775	7.90955666734	-0.483028182364	-0.322336984777	0.726033589181	1.04998313476	0.732238616655	-0.184202459928	0.0728637400225	0.365600886467	-0.259598400187	0.42846494404	0.130500671212	0.0391808855762	0.416799659799	-0.0375422049618	0.54760197934	-39.763	-0.377	-24.698
54	3.84030295982	1.43340460795	-0.462663637364	7.34668064021	3.8133899421	4.83259938664	0.128380274341	-0.164141015317	1.18240114317	0.296375926093	0.0150201239776	1.12670540945	-0.73809909633	-0.408423058209	-0.117524805375	0.434713984769	0.084709971458	0.0717422105988	0.419156298362	-0.113994205769	0.673023232944	-32.089	2.098	-19.956
55	2.85736610446	-0.936958710833	1.35675867845	2.5222345298	0.111471404029	2.53270330456	0.0469720333449	-0.60500046842	0.258829269317	0.278525464732	-0.0140482910656	0.209858762274	-0.180114395102	-0.414423762186	-0.0256409413026	0.300240917964	-0.000508068229106	0.0590498284031	0.365008154379	-0.0578214054522	0.317282881083	-35.982	-17.18	-17.131
56	4.6120932157	2.83926916691	4.96299585326	2.50145709225	2.18875994406	5.36190237889	0.706201229285	-1.68277468462	0.128473917751	0.688994866218	-0.460610196007	0.210787129168	0.462672124024	-0.520834387921	-0.311669349206	0.510226784132	-0.0641569483837	0.030457827514	0.519406805141	0.0519513028904	0.330223075135	-32.855	-26.946	-8.878
57	6.78570242964	6.35430212584	5.64218091817	5.94143422865	5.277656921	4.69098164201	0.0646137965714	-1.17526676576	0.666348138802	1.35125490016	0.502820614586	2.12624135621	0.141790902498	-1.83185909336	-0.505773357805	0.49597604432	-0.040176730679	0.0860030583069	0.845131284204	0.136936807178	0.629306511371	-50.523	-27.792	-16.242

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 203:208 )	A	203 - 208
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 209:215 )	A	209 - 215
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 220:230 )	A	220 - 230
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 231:329 )	A	231 - 329
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 330:338 )	A	330 - 338
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 339:364 )	A	339 - 364
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 365:391 )	A	365 - 391
8	X-RAY DIFFRACTION	8	( CHAIN A AND ( RESID 392:393 OR RESID 401:403 ) )	A	392 - 393
9	X-RAY DIFFRACTION	8	( CHAIN A AND ( RESID 392:393 OR RESID 401:403 ) )	A	401 - 403
10	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 14:29 )	B	14 - 29
11	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 30:54 )	B	30 - 54
12	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 55:75 )	B	55 - 75
13	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 76:81 )	B	76 - 81
14	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 82:103 )	B	82 - 103
15	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 104:124 )	B	104 - 124
16	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 125:128 )	B	125 - 128
17	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 129:162 )	B	129 - 162
18	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 163:190 )	B	163 - 190
19	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 191:207 )	B	191 - 207
20	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 208:219 )	B	208 - 219
21	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 220:232 )	B	220 - 232
22	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 233:286 )	B	233 - 286
23	X-RAY DIFFRACTION	22	( CHAIN B AND RESID 287:303 )	B	287 - 303
24	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 304:328 )	B	304 - 328
25	X-RAY DIFFRACTION	24	( CHAIN B AND RESID 329:335 )	B	329 - 335
26	X-RAY DIFFRACTION	25	( CHAIN B AND RESID 336:367 )	B	336 - 367
27	X-RAY DIFFRACTION	26	( CHAIN B AND RESID 368:390 )	B	368 - 390
28	X-RAY DIFFRACTION	27	( CHAIN B AND ( RESID 391:393 OR RESID 401:404 ) )	B	391 - 393
29	X-RAY DIFFRACTION	27	( CHAIN B AND ( RESID 391:393 OR RESID 401:404 ) )	B	401 - 404
30	X-RAY DIFFRACTION	28	( CHAIN C AND RESID 13:38 )	C	13 - 38
31	X-RAY DIFFRACTION	29	( CHAIN C AND RESID 39:69 )	C	39 - 69
32	X-RAY DIFFRACTION	30	( CHAIN C AND RESID 70:96 )	C	70 - 96
33	X-RAY DIFFRACTION	31	( CHAIN C AND RESID 97:103 )	C	97 - 103
34	X-RAY DIFFRACTION	32	( CHAIN C AND RESID 104:120 )	C	104 - 120
35	X-RAY DIFFRACTION	33	( CHAIN C AND RESID 121:124 )	C	121 - 124
36	X-RAY DIFFRACTION	34	( CHAIN C AND RESID 130:133 )	C	130 - 133
37	X-RAY DIFFRACTION	35	( CHAIN C AND RESID 134:189 )	C	134 - 189
38	X-RAY DIFFRACTION	36	( CHAIN C AND RESID 190:207 )	C	190 - 207
39	X-RAY DIFFRACTION	37	( CHAIN C AND RESID 208:216 )	C	208 - 216
40	X-RAY DIFFRACTION	38	( CHAIN C AND RESID 217:248 )	C	217 - 248
41	X-RAY DIFFRACTION	39	( CHAIN C AND RESID 249:269 )	C	249 - 269
42	X-RAY DIFFRACTION	40	( CHAIN C AND RESID 270:293 )	C	270 - 293
43	X-RAY DIFFRACTION	41	( CHAIN C AND RESID 294:301 )	C	294 - 301
44	X-RAY DIFFRACTION	42	( CHAIN C AND RESID 302:338 )	C	302 - 338
45	X-RAY DIFFRACTION	43	( CHAIN C AND RESID 339:356 )	C	339 - 356
46	X-RAY DIFFRACTION	44	( CHAIN C AND RESID 357:363 )	C	357 - 363
47	X-RAY DIFFRACTION	45	( CHAIN C AND RESID 368:387 )	C	368 - 387
48	X-RAY DIFFRACTION	46	( CHAIN C AND RESID 388:391 )	C	388 - 391
49	X-RAY DIFFRACTION	47	( CHAIN A AND RESID 14:28 )	A	14 - 28
50	X-RAY DIFFRACTION	48	( CHAIN A AND RESID 29:35 )	A	29 - 35
51	X-RAY DIFFRACTION	49	( CHAIN A AND RESID 36:52 )	A	36 - 52
52	X-RAY DIFFRACTION	50	( CHAIN A AND RESID 53:74 )	A	53 - 74
53	X-RAY DIFFRACTION	51	( CHAIN A AND RESID 75:96 )	A	75 - 96
54	X-RAY DIFFRACTION	52	( CHAIN A AND RESID 97:120 )	A	97 - 120
55	X-RAY DIFFRACTION	53	( CHAIN A AND RESID 121:127 )	A	121 - 127
56	X-RAY DIFFRACTION	54	( CHAIN A AND RESID 128:134 )	A	128 - 134
57	X-RAY DIFFRACTION	55	( CHAIN A AND RESID 135:175 )	A	135 - 175
58	X-RAY DIFFRACTION	56	( CHAIN A AND RESID 176:197 )	A	176 - 197
59	X-RAY DIFFRACTION	57	( CHAIN A AND RESID 198:202 )	A	198 - 202

+
About Yorodumi

-
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, 3 molecules ABC

-
Non-polymers , 5 types, 224 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 3 molecules ABC

-Non-polymers , 5 types, 224 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 224 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