PDB-8i83: Crystal Structure of phosphinothricin dehydrogenase

ID or keywords:

Entry

Database: PDB / ID: 8i83

Title

Crystal Structure of phosphinothricin dehydrogenase

Components

Glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / Phosphinothricin dehydrogenase / glufosinate dehydrogenase / amino acid dehydrogenase

Function / homology

Function and homology information

glutamate dehydrogenase (NAD+) activity / amino acid metabolic process / nucleotide binding
Similarity search - Function

Biological species

Lysinibacillus composti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.62 Å

Authors

Cheng, F. / Xue, Y.P. / Zheng, Y.G. / Zou, S.P.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of phosphinothricin dehydrogenase
Authors: Cheng, F. / Xue, Y.P. / Zheng, Y.G.

History

Deposition	Feb 3, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Feb 14, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8i83.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8i83.ent.gz	760.4 KB	Display	PDB format
PDBx/mmJSON format	8i83.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8i83_validation.pdf.gz	487.7 KB	Display	wwPDB validaton report
Full document	8i83_full_validation.pdf.gz	515.5 KB	Display
Data in XML	8i83_validation.xml.gz	81.9 KB	Display
Data in CIF	8i83_validation.cif.gz	112.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i8/8i83 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i83	HTTPS FTP

-
Related structure data

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

Deposited unit

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

F: Glutamate dehydrogenase

E: Glutamate dehydrogenase

hetero molecules

281 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

D: Glutamate dehydrogenase

F: Glutamate dehydrogenase

hetero molecules

E: Glutamate dehydrogenase

C: Glutamate dehydrogenase

defined by author&software
281 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.130, 126.667, 223.741
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Glutamate dehydrogenase Mass: 46799.215 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysinibacillus composti (bacteria) / Gene: EBB45_13425 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N9UCW8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis Tris Propane, pH 6.5, 0.2 M Sodium malonate dibasicmonohydrate, 20% w/v PEG 3350, 10 % v/v Ethylene glycol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2023
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.62→48.22 Å / Num. obs: 81285 / % possible obs: 99.1 % / Redundancy: 7.9 % / B_iso Wilson estimate: 38.74 Å² / CC_1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 13.67
Reflection shell	Resolution: 2.62→2.714 Å / Mean I/σ(I) obs: 2.25 / Num. unique obs: 8009 / CC_1/2: 0.703 / CC star: 0.909 / % possible all: 98.71

-
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: 2.62→48.22 Å / SU ML: 0.3411 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2502	4027	4.96 %
R_work	0.1976	77234	-
obs	0.2002	81261	99.12 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 48.25 Å²

Refinement step

Cycle: LAST / Resolution: 2.62→48.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18425	0	4	436	18865

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	18760
X-RAY DIFFRACTION	f_angle_d	0.496	25363
X-RAY DIFFRACTION	f_chiral_restr	0.04	2838
X-RAY DIFFRACTION	f_plane_restr	0.0043	3286
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0549	6976

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.62-2.65	0.3325	121	0.2711	2689	X-RAY DIFFRACTION	99.57
2.65-2.68	0.3303	122	0.2609	2597	X-RAY DIFFRACTION	98.12
2.68-2.72	0.3256	141	0.254	2608	X-RAY DIFFRACTION	98.5
2.72-2.75	0.3119	129	0.2472	2645	X-RAY DIFFRACTION	100
2.75-2.79	0.2745	142	0.244	2682	X-RAY DIFFRACTION	99.89
2.79-2.83	0.2813	143	0.2398	2642	X-RAY DIFFRACTION	99.86
2.83-2.87	0.3028	151	0.243	2644	X-RAY DIFFRACTION	99.96
2.87-2.92	0.2895	147	0.239	2613	X-RAY DIFFRACTION	99.93
2.92-2.97	0.295	141	0.2285	2682	X-RAY DIFFRACTION	99.93
2.97-3.02	0.2584	133	0.2271	2644	X-RAY DIFFRACTION	99.86
3.02-3.07	0.2692	152	0.2206	2656	X-RAY DIFFRACTION	99.89
3.07-3.13	0.2759	158	0.2346	2623	X-RAY DIFFRACTION	99.82
3.13-3.19	0.3092	150	0.223	2645	X-RAY DIFFRACTION	99.61
3.19-3.26	0.3037	122	0.2163	2703	X-RAY DIFFRACTION	99.68
3.26-3.34	0.2743	126	0.2176	2664	X-RAY DIFFRACTION	99.54
3.34-3.42	0.2963	134	0.2245	2653	X-RAY DIFFRACTION	99.32
3.42-3.52	0.3193	135	0.2204	2633	X-RAY DIFFRACTION	97.64
3.52-3.62	0.2645	158	0.1988	2611	X-RAY DIFFRACTION	99.64
3.62-3.74	0.2499	120	0.1857	2685	X-RAY DIFFRACTION	99.61
3.74-3.87	0.2327	139	0.1848	2670	X-RAY DIFFRACTION	99.65
3.87-4.02	0.274	139	0.1793	2669	X-RAY DIFFRACTION	99.47
4.02-4.21	0.2271	142	0.1717	2674	X-RAY DIFFRACTION	99.12
4.21-4.43	0.1715	140	0.1525	2655	X-RAY DIFFRACTION	98.83
4.43-4.71	0.1773	149	0.1493	2660	X-RAY DIFFRACTION	98.25
4.71-5.07	0.254	127	0.1624	2648	X-RAY DIFFRACTION	96.82
5.07-5.58	0.2321	144	0.1816	2701	X-RAY DIFFRACTION	99.23
5.58-6.38	0.2573	138	0.206	2728	X-RAY DIFFRACTION	99.03
6.38-8.04	0.2183	128	0.183	2756	X-RAY DIFFRACTION	98.83
8.04-48.22	0.1887	156	0.1714	2754	X-RAY DIFFRACTION	95.47

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	0.712645314042	0.0410696204593	-0.0426810994129	0.983532944272	-0.217563373606	0.890463940532	-0.0110839677057	0.0390029906622	-0.0451731271184	-0.0927579576968	-0.0281217496203	0.0950536792105	0.00300799816369	-0.0640873375341	0.0248565162128	0.225764087428	-0.00361809421495	-0.0246669752216	0.261054432397	-0.0420215999285	0.265590290797	14.756274132	8.40466952379	59.1781270956
2	2.57524027747	-0.788500536876	0.825564730637	0.8330539373	-0.0650176577476	1.00382073611	0.235509463679	0.68235546666	-0.196847644916	-0.302107492944	-0.24816865455	0.151660640347	-0.0459910019959	0.0837438643267	0.00930182994127	0.386839526925	0.0683677497829	-0.0255953926072	0.412345733641	-0.0534386534189	0.345797257049	10.4474778262	23.0375848466	41.2448869301
3	0.758505562904	0.366116339746	0.445021745911	0.856715929272	0.110054754088	1.25605828115	-0.0305920314394	-0.205374246499	0.0344133672542	0.124298767525	-0.0321633626045	0.17426586637	-0.146358925303	-0.245608253484	0.0538182246173	0.249698583484	0.0509482261829	0.0198397729783	0.376335856839	-0.043653345017	0.2633530169	2.2068296524	22.6281723377	93.1149058673
4	1.06868003832	-0.160323118978	-0.623248104004	1.23505527547	0.229673742389	1.64290345954	0.186086275242	0.0902675426536	0.120009589083	-0.0698989723156	-0.0202867309282	0.105787318744	-0.469575979024	0.101803067062	-0.112719289087	0.539727731071	0.0962993998186	0.0395714358751	0.463078376256	0.0394852121265	0.431782023831	-16.452531197	50.8181379353	89.0183951465
5	0.901346267507	-0.396312967104	-0.264927474475	0.909508532402	0.250279484018	0.0388993840914	0.00200939101546	0.0989745281467	0.0811033334381	0.00272757793276	-0.037245560205	0.117432437333	-0.0990312259068	-0.215185779735	0.0198053355886	0.325025267522	0.0849698309953	-0.035026736192	0.4842252373	-0.0200471164615	0.268687194522	-11.1514211325	32.189529563	79.5530645306
6	0.725762812888	0.270485058555	0.325492944581	1.0389361557	0.0598620251637	0.937406173303	0.0337624633663	0.158768849579	0.00147509437659	-0.209216752262	-0.0138147242193	-0.143381543056	0.0090582959825	0.0582848055581	-0.0154984092395	0.322199285158	0.0153034999683	0.0909756961165	0.356310081709	-0.0188722784378	0.263713073817	-8.52168770553	49.2563598148	121.634530868
7	0.85395490885	0.228679991226	0.442159368231	0.339108751793	0.523256887652	1.4505925087	-0.0931547694078	0.495998666793	0.248116052241	-0.339520152747	0.148267632606	-0.258098196247	-0.273203737831	0.53122981807	-0.0601304571397	0.578564767451	-0.111992631612	0.206201216892	0.659934311193	0.110808770347	0.607221068714	6.41673682084	65.4161049518	108.505712303
8	0.839963954883	-0.17011688341	0.180745465498	0.713086347745	0.120868779873	0.914495118684	0.0572640971908	-0.121874326683	-0.149761354952	0.159546045565	-0.078704091102	0.182618323218	0.122212233671	-0.181824583372	0.018628307538	0.32921730675	-0.0469676457172	0.060058591441	0.330744518241	0.0212005283763	0.309187326477	4.35889473249	-2.24443116981	96.9968735992
9	1.14433659187	0.161066954383	-0.850294640133	1.37035127978	0.0200977741142	0.661894107477	-0.0483528328172	-0.161149533543	-1.23628868466	0.976968167664	0.301094410406	-0.00157089493212	0.523063386253	-0.683539723409	-0.120683408111	1.33216748256	-0.284597158147	0.0990155927621	0.738714823803	0.145607313974	1.01404493574	8.01767200391	-25.7702570865	116.773033421
10	0.865265518145	0.110229163424	-0.511797645787	1.90612346784	0.531968369268	1.24609045879	-0.0127272813859	-0.146936978671	-0.253247660525	0.738820706132	-0.170154315216	0.148759827236	0.533883007671	-0.398775169637	0.139117447773	0.661595139975	-0.105445859869	0.0282909493629	0.523090751236	0.0206427382895	0.383094869304	12.7227004984	-11.7116680404	112.906484989
11	0.391414162805	-0.227485305087	-0.00181516634596	1.3285971162	-0.190366021898	0.748953435518	-0.256723808099	-0.183883281286	0.143283058307	0.561711894266	0.256302417229	-0.109461297984	-0.145263389897	0.192947220041	-0.0160422687843	0.380182461155	-0.0230059422636	-0.0854029433367	0.313896836542	-0.0666197895195	0.310472946248	38.5618379779	37.1502687076	94.8046898882
12	0.409127684528	-0.462607971825	-0.271325217075	1.30543424752	-0.0270895495856	1.19707170678	0.0253487278691	0.0277250181224	-0.0303100114051	-0.029712073575	-0.0303338451035	-0.136280674505	-0.0907212863904	0.0603949608331	0.00900214044687	0.239333498737	-0.0138694690743	-0.047540827391	0.252880626267	-0.0245894585033	0.300690197932	40.1590935636	26.4026510307	79.4188614581
13	0.569643352957	-0.357455644963	0.360038131594	1.09904153831	0.544174430148	0.858466355754	-0.0170576152222	0.126435464293	0.0250090897785	-0.128633898155	0.0731741930064	0.0441590409807	-0.0330918714934	0.0233482536021	-0.0366165219249	0.266296078464	0.0221816941437	-0.0029198183478	0.228314514886	-0.0244922585274	0.18067328433	30.4066751104	26.7882460425	68.7024569716
14	1.48920283195	0.221872429626	-0.443041924557	0.552617162627	-0.0373878206695	0.899655484387	0.111217555156	-0.0607977913551	0.0188217534465	-0.199892600682	-0.0739537953816	-0.0624175935643	-0.231701011678	0.0326543694536	-0.0247863703075	0.437424406061	-0.0387808292716	-0.00595832908935	0.276773166534	0.00509360001505	0.388673193644	41.7023274097	51.9981428321	67.8848407216
15	0.898538599052	-0.438810271875	-0.21502620755	1.25311692908	0.161050374829	1.62898550362	0.0219208891351	-0.0239587165266	-0.0125557794091	-0.181904538746	0.0358444999324	-0.253896667267	-0.193552117826	0.263818175828	-0.0319321151399	0.409467111886	-0.0654957471927	-0.00516873439476	0.285575609764	0.0260424565237	0.502461987385	52.5621121042	48.8820368283	68.974496701
16	1.17860052492	0.532113763625	-0.378827131969	1.14629260059	0.220703925211	0.691987856272	0.0291929159584	-0.115049930875	0.115611522522	0.0302769816505	-0.0201131646148	0.0110487635864	-0.239958971113	0.0504328477012	-0.00533152127556	0.35660297071	-0.00261322169458	-0.0291312958146	0.2075363935	0.0110897798532	0.285434750181	35.8255810967	46.0694837153	78.266637284
17	1.58237200631	0.478144137607	0.546456581505	2.16120087507	0.734947928879	2.15321632066	-0.0525234635351	0.0844912301156	0.2657667791	-0.184875535943	0.15174700601	0.0307863848886	-0.540652981095	-0.112383024612	-0.157458835899	0.346490959547	0.0309211014204	-0.0296187140633	0.267744923949	0.0199395621389	0.390304720669	25.5787688979	49.8767357422	75.8704339492
18	1.26748162819	1.2508786571	0.0167040081324	2.43417378377	-0.50066243725	0.347721579493	0.122916790965	-0.00820039282909	0.164832124717	0.480811552708	0.0974233091047	0.0450411912494	-0.527209780413	-0.132883852352	-0.131368630353	0.431401691829	0.0537367237436	0.00666455889532	0.290345606354	-0.0854422825839	0.351652052425	26.7723229205	43.5544210548	93.738023882
19	0.377022109878	0.212801802253	-0.155140231068	1.09818203751	0.119379670641	0.572292823876	-0.0267657836461	-0.0107397845189	-0.0806200542411	0.00751357239153	-0.0248446473816	0.11038855881	0.116216148267	-0.0366492716252	0.0407134557142	0.265219860443	-0.00951821617707	0.00843866167868	0.263697584879	0.0246001669063	0.317185023224	-32.9578973762	52.904980509	40.0536961998
20	1.6747309511	0.598477460391	0.125131866168	1.04385512177	0.083516919436	1.2046064332	0.112636190765	-0.043473423813	-0.0573013389112	0.0634534238573	0.0368691559663	0.289194861689	0.0814990935984	-0.302378228178	-0.133939570758	0.492294625683	-0.0387910584892	0.0429958525211	0.385534053166	0.0606255869886	0.54986491296	-49.2860137535	31.1009121073	42.2726052756
21	0.535985646283	0.265991902482	0.0975156465421	1.36270718726	-0.252573779602	0.58663095502	-0.0901299729367	0.0411755255996	-0.116254662477	-0.0951271317611	0.0577025512032	-0.0336805447331	0.125188729268	-0.0984773146788	0.0340392569299	0.332308892671	-0.0262081759338	0.0214532676466	0.280109738527	-0.0401977045103	0.407715506976	-32.5284818	37.7387260913	31.2665512043
22	1.11279675285	1.14422284745	-0.412915205907	1.47279006883	-0.284750546125	0.725479694442	-0.00849145524847	0.222506638759	-0.227854874559	-0.0359018129008	0.0554421811154	-0.103325911004	0.183359246937	0.0275219412626	-0.0321658415853	0.410507081966	0.0490333168611	0.0646688789319	0.332144228034	-0.0212678400408	0.396989068151	-17.5204363579	39.9934221998	36.1586974797

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 199 )	A	A	-1 - 199	1 - 201
2	2	chain 'A' and (resid 200 through 408 )	A	A	200 - 408	202 - 410
3	3	chain 'B' and (resid 1 through 182 )	B	B	1 - 182	1 - 182
4	4	chain 'B' and (resid 183 through 281 )	B	B	183 - 281	183 - 281
5	5	chain 'B' and (resid 282 through 408 )	B	B	282 - 408	282 - 408
6	6	chain 'C' and (resid -1 through 182 )	C	C	-1 - 182	1 - 184
7	7	chain 'C' and (resid 183 through 408 )	C	C	183 - 408	185 - 410
8	8	chain 'D' and (resid -1 through 182 )	D	D	-1 - 182	1 - 184
9	9	chain 'D' and (resid 183 through 215 )	D	D	183 - 215	185 - 217
10	10	chain 'D' and (resid 216 through 408 )	D	D	216 - 408	218 - 322
11	11	chain 'F' and (resid -4 through 40 )	F	E	-4 - 40	1 - 45
12	12	chain 'F' and (resid 41 through 159 )	F	E	41 - 159	46 - 164
13	13	chain 'F' and (resid 160 through 182 )	F	E	160 - 182	165 - 187
14	14	chain 'F' and (resid 183 through 242 )	F	E	183 - 242	188 - 247
15	15	chain 'F' and (resid 243 through 296 )	F	E	243 - 296	248 - 301
16	16	chain 'F' and (resid 297 through 356 )	F	E	297 - 356	302 - 361
17	17	chain 'F' and (resid 357 through 382 )	F	E	357 - 382	362 - 387
18	18	chain 'F' and (resid 383 through 410 )	F	E	383 - 410	388 - 415
19	19	chain 'E' and (resid -4 through 199 )	E	G	-4 - 199	1 - 204
20	20	chain 'E' and (resid 200 through 306 )	E	G	200 - 306	205 - 311
21	21	chain 'E' and (resid 307 through 382 )	E	G	307 - 382	312 - 387
22	22	chain 'E' and (resid 383 through 408 )	E	G	383 - 408	388 - 413

-
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