PDB-3txx: Crystal structure of putrescine transcarbamylase from Enterococcu...

ID or keywords:

Entry

Database: PDB / ID: 3txx

Title

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis

Components

Putrescine carbamoyltransferase

Keywords

TRANSFERASE

Function / homology

Function and homology information

putrescine carbamoyltransferase / putrescine biosynthetic process from arginine via N-carbamoylputrescine /

putrescine carbamoyltransferase activity /

ornithine carbamoyltransferase activity /

amino acid binding /

cytoplasm
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.2 Å

Authors

Shi, D. / Yu, X. / Zhao, G. / Allewell, N.M. / Tuchman, M.

Citation

Journal: To be Published
Title: Crystal structure of putrescine transcarbamylase from Enterococcus faecalis: Structural insights into the oligomeric assembly and the active site
Authors: Shi, D. / Yu, X. / Zhao, G. / Ho, J. / Lu, S. / Allewell, N.M. / Tuchman, M.

History

Deposition	Sep 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 1, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3txx.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb3txx.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	3txx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/3txx ftp://data.pdbj.org/pub/pdb/validation_reports/tx/3txx	HTTPS FTP

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Related structure data

Similar structure data	4a8h-1 6ovw-1 2otc-2 4jqo-d 4a8p-2 4jhx-d 2otc-1 4am8-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (6)

Deposited unit

A: Putrescine carbamoyltransferase

B: Putrescine carbamoyltransferase

C: Putrescine carbamoyltransferase

D: Putrescine carbamoyltransferase

E: Putrescine carbamoyltransferase

F: Putrescine carbamoyltransferase

G: Putrescine carbamoyltransferase

H: Putrescine carbamoyltransferase

I: Putrescine carbamoyltransferase

J: Putrescine carbamoyltransferase

K: Putrescine carbamoyltransferase

L: Putrescine carbamoyltransferase

hetero molecules

489 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putrescine carbamoyltransferase

B: Putrescine carbamoyltransferase

C: Putrescine carbamoyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Putrescine carbamoyltransferase

E: Putrescine carbamoyltransferase

F: Putrescine carbamoyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Putrescine carbamoyltransferase

H: Putrescine carbamoyltransferase

I: Putrescine carbamoyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Putrescine carbamoyltransferase

K: Putrescine carbamoyltransferase

L: Putrescine carbamoyltransferase

hetero molecules

defined by author&software
122 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	273.856, 87.791, 241.299
Angle α, β, γ (deg.)	90.000, 114.080, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	A	1 - 78
1	2	1	chain A and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	A	84 - 235
1	3	1	chain A and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	A	238 - 339
2	1	1	chain B and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	B	1 - 78
2	2	1	chain B and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	B	84 - 235
2	3	1	chain B and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	B	238 - 339
3	1	1	chain C and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	C	1 - 78
3	2	1	chain C and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	C	84 - 235
3	3	1	chain C and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	C	238 - 339
4	1	1	chain D and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	D	1 - 78
4	2	1	chain D and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	D	84 - 235
4	3	1	chain D and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	D	238 - 339
5	1	1	chain E and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	E	1 - 78
5	2	1	chain E and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	E	84 - 235
5	3	1	chain E and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	E	238 - 339
6	1	1	chain F and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	F	1 - 78
6	2	1	chain F and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	F	84 - 235
6	3	1	chain F and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	F	238 - 339
7	1	1	chain G and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	G	1 - 78
7	2	1	chain G and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	G	84 - 235
7	3	1	chain G and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	G	238 - 339
8	1	1	chain H and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	H	1 - 78
8	2	1	chain H and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	H	84 - 235
8	3	1	chain H and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	H	238 - 339
9	1	1	chain I and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	I	1 - 78
9	2	1	chain I and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	I	84 - 235
9	3	1	chain I and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	I	238 - 339
10	1	1	chain J and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	J	1 - 78
10	2	1	chain J and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	J	84 - 235
10	3	1	chain J and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	J	238 - 339
11	1	1	chain K and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	K	1 - 78
11	2	1	chain K and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	K	84 - 235
11	3	1	chain K and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	K	238 - 339
12	1	1	chain L and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	L	1 - 78
12	2	1	chain L and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	L	84 - 235
12	3	1	chain L and (resseq 1:78 or resseq 84:235 or resseq 238:339 )	L	238 - 339

#1: Protein	Putrescine carbamoyltransferase / / PTC / PTCase / Agmatine catabolism protein B / Putrescine transcarbamoylase / Putrescine transcarbamylase Mass: 40556.805 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: agcB, argF-2, EF_0732, ptcA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q837U7, putrescine carbamoyltransferase
#2: Chemical	... ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO₄

#1: Protein

Putrescine carbamoyltransferase /

/ PTC / PTCase / Agmatine catabolism protein B / Putrescine transcarbamoylase / Putrescine transcarbamylase

Mass: 40556.805 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterococcus faecalis (bacteria) / Gene: agcB, argF-2, EF_0732, ptcA / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q837U7,

putrescine carbamoyltransferase

#2: Chemical

...
ChemComp-SO4 / SULFATE ION /

Sulfate

Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.79 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 200 mM Magnesium sulfate, 15-17% PEG 3350 and 100 mM Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 291 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2006
Details: focusing monochrometer and vertical focusing mirror

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 3.2→50 Å / Num. all: 86740 / Num. obs: 85439 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_merge(I) obs: 0.12 / Χ²: 1.017 / Net I/σ(I): 6.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3.2-3.31	2.7	0.468	7503	0.925	1	87.4
3.31-3.45	3.2	0.403	8403	1.039	1	97.8
3.45-3.6	3.6	0.328	8651	1.039	1	100
3.6-3.79	3.7	0.247	8611	1.087	1	100
3.79-4.03	3.8	0.182	8608	1.042	1	100
4.03-4.34	3.8	0.126	8664	0.946	1	100
4.34-4.78	3.7	0.099	8658	1.027	1	100
4.78-5.47	3.7	0.096	8698	1.025	1	100
5.47-6.89	3.7	0.09	8738	1.016	1	100
6.89-50	3.6	0.047	8905	0.99	1	99.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction
CBASS		data collection
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→48.17 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8148 / SU ML: 0.9 / σ(F): 1.34 / σ(I): 0 / Phase error: 25.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2343	1998	2.34 %	Random
R_work	0.1895	-	-	-
all	0.201	85439	-	-
obs	0.1905	85319	98.06 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.998 Å² / k_sol: 0.318 e/Å³

Displacement parameters

B_iso max: 301.21 Å² / B_iso mean: 82.6604 Å² / B_iso min: 9.05 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-12.729 Å²	0 Å²	11.0771 Å²
2-	-	12.6059 Å²	-0 Å²
3-	-	-	0.123 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→48.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	32007	0	135	0	32142

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	32676
X-RAY DIFFRACTION	f_angle_d	1.269	44100
X-RAY DIFFRACTION	f_chiral_restr	0.08	4886
X-RAY DIFFRACTION	f_plane_restr	0.007	5739
X-RAY DIFFRACTION	f_dihedral_angle_d	18.619	12116

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2610	X-RAY DIFFRACTION	POSITIONAL	0.053
1	2	B	2610	X-RAY DIFFRACTION	POSITIONAL	0.053
1	3	C	2607	X-RAY DIFFRACTION	POSITIONAL	0.048
1	4	D	2607	X-RAY DIFFRACTION	POSITIONAL	0.054
1	5	E	2565	X-RAY DIFFRACTION	POSITIONAL	0.054
1	6	F	2600	X-RAY DIFFRACTION	POSITIONAL	0.051
1	7	G	2600	X-RAY DIFFRACTION	POSITIONAL	0.049
1	8	H	2585	X-RAY DIFFRACTION	POSITIONAL	0.048
1	9	I	2556	X-RAY DIFFRACTION	POSITIONAL	0.048
1	10	J	2592	X-RAY DIFFRACTION	POSITIONAL	0.054
1	11	K	2600	X-RAY DIFFRACTION	POSITIONAL	0.054
1	12	L	2600	X-RAY DIFFRACTION	POSITIONAL	0.055

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.2-3.279	0.4059	118	0.338	4892	5010	81
3.279-3.3676	0.4068	136	0.2814	5701	5837	95
3.3676-3.4667	0.3031	143	0.2492	5983	6126	99
3.4667-3.5785	0.3028	145	0.233	6010	6155	100
3.5785-3.7064	0.3213	143	0.221	6035	6178	100
3.7064-3.8547	0.2353	144	0.2034	6009	6153	100
3.8547-4.0301	0.2608	145	0.193	6046	6191	100
4.0301-4.2424	0.1966	145	0.1646	6048	6193	100
4.2424-4.508	0.1977	145	0.1423	6048	6193	100
4.508-4.8558	0.1683	146	0.131	6077	6223	100
4.8558-5.3439	0.1819	145	0.1576	6071	6216	100
5.3439-6.1158	0.2419	147	0.1941	6103	6250	100
6.1158-7.7002	0.1899	147	0.1736	6111	6258	100
7.7002-48.1759	0.2086	149	0.1846	6187	6336	98

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	0.7619	0.4705	0.0213	0.4539	0.051	0.2989	0.0601	-0.1661	0.1381	0.1198	-0.0153	-0.0745	-0.1309	0.1069	0.0336	-0.0843	-0.3508	0.0152	0.2596	-0.0002	-0.0028	-38.4271	-3.3327	62.2928
2	1.257	0.2198	-0.3421	1.0622	-0.3194	1.0497	-0.0737	-0.1662	-0.0002	0.1798	0.1155	0.0824	-0.0758	0.0411	-0.0084	0.061	-0.1853	0.0313	0.1197	0.1689	0.0315	-71.9715	-19.921	52.4452
3	1.2194	-0.3534	0.4158	1.4318	-0.3396	0.8242	0.0077	-0.1654	0.3077	0.084	0.0408	0.1685	-0.236	-0.0821	-0.0385	0.2886	-0.3645	0.0359	0.3335	0.0475	0.1871	-61.9037	12.9271	37.0162
4	0.5746	0.0422	0.0231	1.364	-0.2832	0.5991	0.0355	-0.0141	0.2245	-0.0277	0.0335	-0.019	-0.1838	0.1194	0.031	0.327	-0.1658	0.0876	-0.0268	-0.0991	0.2522	-121.2092	27.4494	50.9856
5	0.8984	0.0979	-0.0687	0.7988	0.2124	0.5569	0.094	-0.06	0.0264	-0.1213	-0.024	-0.0367	-0.1028	0.1436	0.011	0.0614	-0.2149	-0.1049	-0.0643	0.0145	0.0499	-106.1693	-7.7918	52.5325
6	1.6157	-0.025	0.1602	1.8974	-0.0257	0.9389	0.0211	-0.2833	0.3985	0.2383	0.0057	-0.5811	-0.2264	0.496	-0.0042	0.5032	-0.4215	0.0065	0.4259	-0.2377	0.384	-94.9339	18.4283	77.1968
7	2.1017	0.8056	0.2733	1.768	0.1272	1.261	0.1846	-0.365	-0.1283	0.1192	-0.0607	0.4001	0.1893	-0.1091	-0.1207	0.2464	0.0818	0.004	0.3151	0.0051	0.2946	-123.8286	9.374	-20.868
8	0.9033	-0.2112	-0.3061	1.0623	0.2739	1.4839	0.1393	-0.4372	0.2144	0.4676	-0.0276	0.2774	-0.0853	0.0695	-0.0423	0.364	-0.1077	0.256	0.4498	-0.1658	0.1688	-104.6729	30.4889	4.6183
9	1.1565	-0.183	0.136	1.5657	-0.4018	1.0353	0.1244	-0.3224	-0.115	0.3528	-0.0829	-0.0056	0.2454	0.1149	-0.0169	0.3125	0.1194	-0.056	0.4105	-0.0554	0.0278	-90.0548	-2.4038	-8.1994
10	0.1556	0.0997	-0.1632	0.4178	0.1207	0.3499	0.0066	0.0631	0.2358	0.0305	-0.0004	0.3056	-0.1768	-0.194	-0.0016	0.2295	0.0493	0.0623	0.3782	0.0663	0.2912	-26.7369	49.9283	83.6705
11	1.0538	0.0697	-0.2264	1.0222	0.0618	1.6419	0.0611	-0.4118	0.262	0.4776	0.1053	0.1859	-0.3179	-0.1449	-0.0346	0.4423	-0.081	0.1994	0.2822	-0.0487	0.0043	-1.8439	49.5919	112.7888
12	1.6473	-0.1395	0.0741	1.6051	0.1454	1.3051	-0.0503	-0.1796	-0.2936	0.2584	0.0454	0.2081	0.5072	-0.3235	-0.0349	0.4146	-0.2084	0.0469	0.3981	-0.0743	0.1505	-7.1931	18.0663	91.5287

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A	A	0 - 339
2	X-RAY DIFFRACTION	2	chain B	B	-13 - 339
3	X-RAY DIFFRACTION	3	chain C	C	0 - 339
4	X-RAY DIFFRACTION	4	chain D	D	-7 - 339
5	X-RAY DIFFRACTION	5	chain E	E	-12 - 339
6	X-RAY DIFFRACTION	6	chain F	F	0 - 339
7	X-RAY DIFFRACTION	7	chain G	G	-1 - 339
8	X-RAY DIFFRACTION	8	chain H	H	-1 - 339
9	X-RAY DIFFRACTION	9	chain I	I	-1 - 339
10	X-RAY DIFFRACTION	10	chain J	J	-1 - 339
11	X-RAY DIFFRACTION	11	chain K	K	-1 - 339
12	X-RAY DIFFRACTION	12	chain L	L	-1 - 339

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Movie

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Open data

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Links

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Assembly

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Experimental details

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About Yorodumi

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

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

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Yorodumi