PDB-7sy9: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig...

ID or keywords:

Entry

Database: PDB / ID: 7sy9

Title

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1

Components

UDP-N-acetylmuramoylalanine--D-glutamate ligase

Keywords

LIGASE / SSGCID / UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase / MurD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Nov 24, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 15, 2021	Provider: repository / Type: Initial release
Revision 1.1	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	7sy9.cif.gz	389.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7sy9.ent.gz	267.8 KB	Display	PDB format
PDBx/mmJSON format	7sy9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7sy9_validation.pdf.gz	453.1 KB	Display	wwPDB validaton report
Full document	7sy9_full_validation.pdf.gz	457.4 KB	Display
Data in XML	7sy9_validation.xml.gz	29.4 KB	Display
Data in CIF	7sy9_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sy/7sy9 ftp://data.pdbj.org/pub/pdb/validation_reports/sy/7sy9	HTTPS FTP

-
Related structure data

Related structure data	5a5fS S: Starting model for refinement
Similar structure data	4lhb-d 4cvl-d 7sy9-2 1o7f-d 4cvm-d 4isg-d 1ysr-d 5itg-2 4wmt-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: PsaeA.17938.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UDP-N-acetylmuramoylalanine--D-glutamate ligase

B: UDP-N-acetylmuramoylalanine--D-glutamate ligase

hetero molecules

96.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: UDP-N-acetylmuramoylalanine--D-glutamate ligase

hetero molecules

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

2

B: UDP-N-acetylmuramoylalanine--D-glutamate ligase

hetero molecules

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

Unit cell

Length a, b, c (Å)	94.750, 94.750, 442.920
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22
Space group name Hall	P6₅2(x,y,z+1/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+5/6 #3: y,-x+y,z+1/6 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: x-y,-y,-z #7: -x,-x+y,-z+1/3 #8: -x,-y,z+1/2 #9: y,x,-z+2/3 #10: -y,-x,-z+1/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+5/6

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and ((resid 8 through 10 and (name N...
d_2	ens_1	(chain "B" and (resid 8 through 94 or (resid 95...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	HIS	THR	A	1 - 31
d_1	2	ens_1	PRO	VAL	A	35 - 48
d_1	3	ens_1	ARG	CYS	A	51 - 61
d_1	4	ens_1	ARG	VAL	A	64 - 177
d_1	5	ens_1	GLY	ALA	A	179 - 433
d_2	1	ens_1	HIS	ALA	D	1 - 425

NCS oper: (Code: givenMatrix: (-0.854372654473, 0.154632996511, -0.496120956702), (-0.293762503805, 0.643805256439, 0.706553878441), (0.428661823174, 0.749402047083, -0.504624229681)Vector: -27. ...

#1: Protein	UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase Mass: 48312.270 Da / Num. of mol.: 2 / Fragment: PsaeA.17938.a.B2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: murD, PA4414 / Plasmid: PsaeA.17938.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9HVZ9, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.98 Å³/Da / Density % sol: 58.7 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Molecular dimensions/Calibre Morpheus screen, condition G6: 10% (w/V) PEG 8000, 20% (V/V) ethylene glycol: 20mM of each sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, ...Details: Molecular dimensions/Calibre Morpheus screen, condition G6: 10% (w/V) PEG 8000, 20% (V/V) ethylene glycol: 20mM of each sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, potassium sodium tartrate tetrahydrate, sodium oxamate: 100mM Sodium HEPES: MOPS (acid) pH 7.5: PsaeA.17938.a.B2.PS38064 at 46mg/ml: tray 320910 g6: cryo: direct: puck hdj1-6.

Crystal

Density Matthews: 2.98 Å³/Da / Density % sol: 58.7 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular dimensions/Calibre Morpheus screen, condition G6: 10% (w/V) PEG 8000, 20% (V/V) ethylene glycol: 20mM of each sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.97741 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2021

Radiation

Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97741 Å / Relative weight: 1

Reflection

Resolution: 2.75→50 Å / Num. obs: 31984 / % possible obs: 99.7 % / Redundancy: 10.538 % / B_iso Wilson estimate: 74.1 Å² / CC_1/2: 1 / R_merge(I) obs: 0.068 / R_rim(I) all: 0.072 / Χ²: 0.958 / Net I/σ(I): 20.79

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.75-2.82	11.486	0.601	3.56	2294	0.937	0.629	100
2.82-2.9	11.278	0.493	4.37	2237	0.947	0.516	100
2.9-2.98	11.253	0.374	5.63	2205	0.978	0.392	100
2.98-3.07	11.647	0.29	7.52	2112	0.983	0.303	100
3.07-3.18	11.344	0.221	9.63	2084	0.99	0.232	100
3.18-3.29	11.111	0.179	12.34	1996	0.992	0.187	99.9
3.29-3.41	10.787	0.141	15.81	1946	0.994	0.148	100
3.41-3.55	11.057	0.116	20.04	1844	0.996	0.122	100
3.55-3.71	10.474	0.102	22.34	1816	0.996	0.108	100
3.71-3.89	10.897	0.083	27.32	1717	0.997	0.087	99.8
3.89-4.1	10.23	0.072	31.22	1668	0.998	0.076	99.8
4.1-4.35	9.414	0.064	32.43	1559	0.998	0.068	99.7
4.35-4.65	9.488	0.057	34.95	1469	0.998	0.06	99.5
4.65-5.02	9.291	0.055	35.92	1403	0.999	0.059	99.9
5.02-5.5	9.777	0.056	35.92	1296	0.998	0.059	99.8
5.5-6.15	9.56	0.051	36.34	1174	0.999	0.054	99.8
6.15-7.1	9.242	0.047	37.16	1059	0.999	0.049	99.2
7.1-8.7	9.285	0.04	40.36	919	0.999	0.042	98.8
8.7-12.3	8.79	0.034	41.67	737	0.999	0.036	97.5
12.3-50	8.281	0.025	40.2	449	1	0.027	90.7

-
Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.20rc3 4406	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
Coot		model building
PHENIX		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 5a5f in two domains as per Morda

5a5f

Resolution: 2.75→47.38 Å / SU ML: 0.3961 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2467	2021	6.34 %	0
R_work	0.2119	29878	-	-
obs	0.2141	31899	99.84 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 81.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→47.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6173	0	10	53	6236

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0044	6277
X-RAY DIFFRACTION	f_angle_d	0.7179	8534
X-RAY DIFFRACTION	f_chiral_restr	0.0476	1010
X-RAY DIFFRACTION	f_plane_restr	0.0063	1126
X-RAY DIFFRACTION	f_dihedral_angle_d	12.5127	2169

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 1.25244498897 Å

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 (%)
2.75-2.82	0.3047	148	0.2628	2075	X-RAY DIFFRACTION	99.96
2.82-2.89	0.2655	126	0.2614	2074	X-RAY DIFFRACTION	100
2.9-2.98	0.3927	133	0.306	2104	X-RAY DIFFRACTION	99.96
2.98-3.08	0.3252	159	0.3042	2050	X-RAY DIFFRACTION	100
3.08-3.19	0.3472	140	0.2673	2100	X-RAY DIFFRACTION	99.96
3.19-3.31	0.2859	144	0.238	2082	X-RAY DIFFRACTION	99.96
3.31-3.46	0.2421	144	0.2379	2096	X-RAY DIFFRACTION	100
3.46-3.65	0.2866	144	0.2492	2141	X-RAY DIFFRACTION	100
3.65-3.88	0.3154	141	0.2369	2093	X-RAY DIFFRACTION	100
3.88-4.17	0.206	154	0.195	2135	X-RAY DIFFRACTION	99.91
4.18-4.59	0.2155	144	0.1675	2135	X-RAY DIFFRACTION	99.56
4.59-5.26	0.1919	154	0.1787	2179	X-RAY DIFFRACTION	99.79
5.26-6.62	0.2241	123	0.2077	2228	X-RAY DIFFRACTION	99.79
6.62-47.38	0.2298	167	0.187	2386	X-RAY DIFFRACTION	99.03

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	2.55469695783	0.340088713589	1.38774654879	1.16417380632	-0.768643562561	5.64538297026	0.203717231764	0.144004762804	0.0467636862393	-0.712086128127	-0.302629831974	0.336868605169	-0.253921559449	-0.362731156847	0.113010557998	0.850351195745	0.206370175066	-0.167101550882	0.62643598946	-0.098191958468	0.55810835568	-48.9606827844	44.4205199834	38.6922479384
2	3.77674567856	0.819703472071	-2.33860883662	1.41611682883	-0.852694496819	2.31754469321	-0.0515839843222	-0.0946711769672	-0.0612699316316	0.164793095009	-0.155235588561	0.19331363598	-0.0788155494465	-0.246491526525	0.203794069741	0.440378435595	0.0158927197013	-0.00905884736216	0.735026742189	-0.144108211035	0.421956336732	-53.5775574039	34.706363993	68.3264373128
3	4.26381122794	0.369986360494	0.612560052999	4.26115690234	2.597139615	2.64609948843	0.173144054269	0.637658716307	2.08611595983	0.492260298809	0.612383764192	-0.5740705063	0.665926502299	0.290975591189	-0.74136509997	0.852180578627	-0.0394397782752	-0.403417813164	0.909893922045	0.0933355839038	1.99143565059	9.50399312115	9.03912554232	60.0169812817
4	2.5716511598	1.1099515275	2.25123459022	6.35490954608	-4.14796722115	7.6358723638	0.219817966642	0.908493397231	-2.03482380459	-1.00851533408	-0.695447286695	-2.63253962634	0.301814318187	1.75280986133	0.101187326493	0.889871087673	0.182192397573	-0.28405984098	1.62909071345	-0.705388731117	2.67493585049	17.29485372	4.02842206668	57.1429574364
5	5.29442000501	-1.80051643109	1.65761178285	1.58183431075	-0.238356990692	3.7726892458	0.991341964061	-0.298504927836	-1.2739962535	0.514250498488	-0.979097855842	-1.82458720402	1.2550877989	-0.0763078814693	-0.221125737463	1.08982528937	-0.212515276564	-0.430978053219	0.903593916868	0.217317616645	2.02871698763	2.80728007516	-3.33703428831	59.654058303
6	3.78407019615	-1.49604217688	1.0715698648	4.95142966036	-1.92873583465	2.97769868041	0.0984224182598	-0.381686955385	-0.825333906824	0.386658440442	-0.0377037264606	-2.1423688111	-0.242120876199	0.407864819186	-0.0460654338897	0.611201774104	-0.208060019985	-0.184956897098	0.666490428925	0.164125191551	1.22029506299	-3.95886292463	19.653200103	54.3372655073
7	4.07657879524	0.454461467262	2.15737393015	3.54963103174	0.401778537053	4.12992644617	0.334953304795	-1.06909467945	-0.87148644566	0.613972291155	-0.416729429186	-0.96725919398	0.657951703892	0.0263493141911	0.0500945121456	0.682189101877	-0.237769308706	-0.105710031001	0.836984673108	0.311177465832	0.890198922722	-12.465984316	8.81809035616	52.7294371435
8	7.8211182422	-5.23913702944	3.42841756888	9.41729498659	-2.16186668657	4.38442620326	0.666813977406	-0.870367584608	-1.11191747392	0.422770482562	-0.341003470443	1.10770745967	0.0677343891483	-0.521457303342	-0.414791427422	0.638995952635	-0.182619178643	0.0311681985417	0.74236349664	0.0727143734478	0.598448191678	-22.8962265142	16.875010787	51.3307791127
9	2.34740372843	1.25785217954	-2.12307982617	1.03885641345	-0.289354815057	8.42706219415	-0.0298784278839	0.0260290553799	-0.0332010608596	-0.087403667098	-0.12331734657	-0.352106461417	-0.365505525155	0.240979609573	0.116532023082	0.477259804646	-0.0242272226175	0.0556508435562	0.397629982606	0.0895354725922	0.49546659398	-12.2666724771	29.4200963015	34.8701573476
10	2.95629777586	-1.02292259053	1.87405215243	7.43886251587	-0.468551444253	6.35149505244	0.0194601607279	0.70552624384	-0.580539823828	-0.93758977287	-0.189256865999	-0.276042439746	0.604778900789	0.71053167793	0.178846023223	0.750463894199	0.0191064582552	0.309637887141	0.594021306386	0.0952439322182	0.622658193195	-4.06801349273	23.5482697004	12.6912043298
11	3.35330162067	1.6299710976	0.772626697094	2.56948373201	0.0689198191928	5.0707476784	-0.438335559975	-0.320535376921	-0.200441737104	0.0512423655812	0.238225318882	-0.6344173415	-0.488817699336	1.07923085784	0.219645495752	0.608479857789	-0.100438929265	0.182911606205	0.81489645814	0.156709616366	0.69714212424	2.47286892095	31.6206293723	23.3791944824

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 8 through 195 )	A	A	8 - 195	1 - 180
2	2	chain 'A' and (resid 196 through 448 )	A	A	196 - 448	181 - 433
3	3	chain 'B' and (resid 8 through 29 )	B	D	8 - 29	1 - 22
4	4	chain 'B' and (resid 30 through 63 )	B	D	30 - 63	23 - 51
5	5	chain 'B' and (resid 64 through 98 )	B	D	64 - 98	52 - 84
6	6	chain 'B' and (resid 99 through 169 )	B	D	99 - 169	85 - 155
7	7	chain 'B' and (resid 170 through 205 )	B	D	170 - 205	156 - 182
8	8	chain 'B' and (resid 206 through 243 )	B	D	206 - 243	183 - 220
9	9	chain 'B' and (resid 244 through 360 )	B	D	244 - 360	221 - 337
10	10	chain 'B' and (resid 361 through 400 )	B	D	361 - 400	338 - 377
11	11	chain 'B' and (resid 401 through 448 )	B	D	401 - 448	378 - 425

-
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

-
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