PDB-2jlm: Structure of a Putative Acetyltransferase (ACIAD1637) from Acinet...

ID or keywords:

Entry

Database: PDB / ID: 2jlm

Title

Structure of a Putative Acetyltransferase (ACIAD1637) from Acinetobacter baylyi ADP1

Components

PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE

Keywords

TRANSFERASE /

PHOSPHINOTHRICIN /

ACETYLTRANSFERASE /

METHIONINE SULFOXIMINE

Function / homology

Function and homology information

N-acetyltransferase activity
Similarity search - Function

Biological species

ACINETOBACTER BAYLYI (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Davies, A.M. / Tata, R. / Snape, A. / Sutton, B.J. / Brown, P.R.

Citation

Journal: Biochimie / Year: 2009
Title: Structure and Substrate Specificity of Acetyltransferase Aciad1637 from Acinetobacter Baylyi Adp1.
Authors: Davies, A.M. / Tata, R. / Snape, A. / Sutton, B.J. / Brown, P.R.

History

Deposition	Sep 10, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 20, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	Jun 12, 2019	Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2jlm.cif.gz	230.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2jlm.ent.gz	187.2 KB	Display	PDB format
PDBx/mmJSON format	2jlm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jl/2jlm ftp://data.pdbj.org/pub/pdb/validation_reports/jl/2jlm	HTTPS FTP

-
Related structure data

Related structure data	2j8mS S: Starting model for refinement
Similar structure data	1lyw-d 5cqr-1 5vmr-d 3s2i-2 6ww2-d 3be1-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE

B: PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE

C: PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE

D: PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE

E: PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE

F: PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.410, 78.410, 197.760
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.45171, 0.89187, -0.02291), (0.89216, -0.45163, 0.00861), (-0.00267, -0.02433, -0.9997)	-11.46824, 18.87809, 29.34303
2	given	(-0.48312, -0.87278, -0.06969), (0.87544, -0.48282, -0.02221), (-0.01426, -0.07174, 0.99732)	41.29008, -24.49101, 0.28364
3	given	(0.56059, -0.82496, -0.07194), (-0.82809, -0.55825, -0.05121), (0.00209, 0.08828, -0.99609)	-14.46264, 67.05414, 29.1847
4	given	(0.99924, 0.02569, -0.02943), (-0.02558, 0.99966, 0.00412), (0.02952, -0.00336, 0.99956)	-34.35027, 24.91047, -67.67772
5	given	(0.4216, 0.90662, -0.01696), (0.90612, -0.42194, -0.03021), (-0.03455, -0.00263, -0.9994)	-4.30338, -22.96282, 96.56022

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein	PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE / PUTATIVE ACETYLTRANSFERASE ACIAD1637 Mass: 20640.459 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACINETOBACTER BAYLYI (bacteria) / Strain: ADP1 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FBS8

#1: Protein

PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE / PUTATIVE ACETYLTRANSFERASE ACIAD1637

Mass: 20640.459 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ACINETOBACTER BAYLYI (bacteria) / Strain: ADP1 / Plasmid: PET / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FBS8

-
Non-polymers , 5 types, 393 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-AZI / AZIDE ION / Azide Mass: 42.020 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N₃
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALS WERE GROWN USING HANGING DROP VAPOR DIFFUSION. RESERVOIR CONTAINED 500 MICROLITRES OF 0.1M TRIS-HCL AT PH6.5, 1.2M SODIUM ACETATE AND 0.1% SODIUM AZIDE. DROPS CONTAINED 1 MICROLITRE ...Details: CRYSTALS WERE GROWN USING HANGING DROP VAPOR DIFFUSION. RESERVOIR CONTAINED 500 MICROLITRES OF 0.1M TRIS-HCL AT PH6.5, 1.2M SODIUM ACETATE AND 0.1% SODIUM AZIDE. DROPS CONTAINED 1 MICROLITRE OF PROTEIN AT A CONCENTRATION OF 8MG/ML TO WHICH AN EQUAL VOLUME OF RESERVOIR WAS ADDED.

Crystal

Density Matthews: 2.86 Å³/Da / Density % sol: 57 % / Description: NONE

Crystal grow

Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE GROWN USING HANGING DROP VAPOR DIFFUSION. RESERVOIR CONTAINED 500 MICROLITRES OF 0.1M TRIS-HCL AT PH6.5, 1.2M SODIUM ACETATE AND 0.1% SODIUM AZIDE. DROPS CONTAINED 1 MICROLITRE ...

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488
Detector	Type: MARRESEARCH / Detector: CCD / Date: Feb 24, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 2.35→68 Å / Num. obs: 56442 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / B_iso Wilson estimate: 31.23 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 17.5
Reflection shell	Resolution: 2.35→2.41 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.25 / Mean I/σ(I) obs: 4 / % possible all: 94.7

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8M

2j8m

Resolution: 2.35→68 Å / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.238	-	5 %
R_work	0.182	-	-
obs	-	56442	99.6 %

Solvent computation

Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 56.83 Å² / k_sol: 0.37 e/Å³

Displacement parameters

B_iso mean: 34.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.032 Å²	0 Å²	-0 Å²
2-	-	1.032 Å²	0 Å²
3-	-	-	-2.065 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8392	0	119	365	8876

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	667
X-RAY DIFFRACTION	f_angle_d	1.029	2645
X-RAY DIFFRACTION	f_dihedral_angle_d	18.952	4574
X-RAY DIFFRACTION	f_chiral_restr	0.066	141
X-RAY DIFFRACTION	f_plane_restr	0.005	247

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3501-2.3536	0.3306	360	X-RAY DIFFRACTION	93
2.3536-2.3571	0.2069	559	X-RAY DIFFRACTION	86
2.3571-2.3606	0.225	376	X-RAY DIFFRACTION	89
2.3606-2.3642	0.2145	484	X-RAY DIFFRACTION	86
2.3642-2.3678	0.1921	455	X-RAY DIFFRACTION	92
2.3678-2.3714	0.176	472	X-RAY DIFFRACTION	90
2.3714-2.375	0.1913	508	X-RAY DIFFRACTION	90
2.375-2.3787	0.2085	428	X-RAY DIFFRACTION	88
2.3787-2.3824	0.1861	492	X-RAY DIFFRACTION	91
2.3824-2.3861	0.1914	467	X-RAY DIFFRACTION	92
2.3861-2.3898	0.2014	346	X-RAY DIFFRACTION	91
2.3898-2.3936	0.1727	464	X-RAY DIFFRACTION	90
2.3936-2.3973	0.1961	469	X-RAY DIFFRACTION	94
2.3973-2.4011	0.1804	460	X-RAY DIFFRACTION	95
2.4011-2.405	0.1754	431	X-RAY DIFFRACTION	94
2.405-2.4088	0.1781	544	X-RAY DIFFRACTION	93
2.4088-2.4127	0.1833	481	X-RAY DIFFRACTION	94
2.4127-2.4166	0.1714	455	X-RAY DIFFRACTION	95
2.4166-2.4205	0.1872	494	X-RAY DIFFRACTION	97
2.4205-2.4244	0.1865	497	X-RAY DIFFRACTION	96
2.4244-2.4284	0.1786	482	X-RAY DIFFRACTION	96
2.4284-2.4324	0.1745	465	X-RAY DIFFRACTION	98
2.4324-2.4364	0.1784	552	X-RAY DIFFRACTION	98
2.4364-2.4405	0.1783	519	X-RAY DIFFRACTION	98
2.4405-2.4446	0.1787	504	X-RAY DIFFRACTION	99
2.4446-2.4487	0.1801	519	X-RAY DIFFRACTION	98
2.4487-2.4528	0.1788	474	X-RAY DIFFRACTION	99
2.4528-2.457	0.1798	465	X-RAY DIFFRACTION	99
2.457-2.4612	0.1761	475	X-RAY DIFFRACTION	100
2.4612-2.4654	0.1896	514	X-RAY DIFFRACTION	100
2.4654-2.4696	0.1874	599	X-RAY DIFFRACTION	100
2.4696-2.4739	0.1734	464	X-RAY DIFFRACTION	100
2.4739-2.4782	0.202	424	X-RAY DIFFRACTION	100
2.4782-2.4826	0.1975	488	X-RAY DIFFRACTION	100
2.4826-2.4869	0.1889	496	X-RAY DIFFRACTION	100
2.4869-2.4913	0.2106	468	X-RAY DIFFRACTION	100
2.4913-2.4958	0.2039	640	X-RAY DIFFRACTION	100
2.4958-2.5002	0.1905	480	X-RAY DIFFRACTION	100
2.5002-2.5047	0.1923	512	X-RAY DIFFRACTION	100
2.5047-2.5092	0.203	468	X-RAY DIFFRACTION	100
2.5092-2.5138	0.2035	556	X-RAY DIFFRACTION	100
2.5138-2.5184	0.2077	498	X-RAY DIFFRACTION	100
2.5184-2.523	0.2104	531	X-RAY DIFFRACTION	100
2.523-2.5277	0.2084	520	X-RAY DIFFRACTION	100
2.5277-2.5324	0.2083	512	X-RAY DIFFRACTION	100
2.5324-2.5371	0.1885	518	X-RAY DIFFRACTION	100
2.5371-2.5419	0.185	400	X-RAY DIFFRACTION	100
2.5419-2.5467	0.1864	512	X-RAY DIFFRACTION	100
2.5467-2.5515	0.1718	524	X-RAY DIFFRACTION	100
2.5515-2.5564	0.1866	498	X-RAY DIFFRACTION	100
2.5564-2.5613	0.1843	548	X-RAY DIFFRACTION	100
2.5613-2.5663	0.1719	427	X-RAY DIFFRACTION	100
2.5663-2.5712	0.1992	512	X-RAY DIFFRACTION	100
2.5712-2.5763	0.1838	488	X-RAY DIFFRACTION	100
2.5763-2.5813	0.1793	572	X-RAY DIFFRACTION	100
2.5813-2.5865	0.189	440	X-RAY DIFFRACTION	100
2.5865-2.5916	0.1891	572	X-RAY DIFFRACTION	100
2.5916-2.5968	0.177	524	X-RAY DIFFRACTION	100
2.5968-2.602	0.1758	520	X-RAY DIFFRACTION	100
2.602-2.6073	0.1801	500	X-RAY DIFFRACTION	100
2.6073-2.6126	0.1793	548	X-RAY DIFFRACTION	100
2.6126-2.618	0.1951	452	X-RAY DIFFRACTION	100
2.618-2.6234	0.1823	504	X-RAY DIFFRACTION	100
2.6234-2.6288	0.1834	524	X-RAY DIFFRACTION	100
2.6288-2.6343	0.1704	440	X-RAY DIFFRACTION	100
2.6343-2.6399	0.1756	458	X-RAY DIFFRACTION	100
2.6399-2.6455	0.1614	528	X-RAY DIFFRACTION	100
2.6455-2.6511	0.1597	516	X-RAY DIFFRACTION	100
2.6511-2.6568	0.1616	504	X-RAY DIFFRACTION	100
2.6568-2.6625	0.1722	588	X-RAY DIFFRACTION	100
2.6625-2.6683	0.1775	424	X-RAY DIFFRACTION	100
2.6683-2.6741	0.1699	527	X-RAY DIFFRACTION	100
2.6741-2.68	0.1718	496	X-RAY DIFFRACTION	100
2.68-2.686	0.182	520	X-RAY DIFFRACTION	100
2.686-2.692	0.1865	556	X-RAY DIFFRACTION	100
2.692-2.698	0.2086	500	X-RAY DIFFRACTION	100
2.698-2.7041	0.1836	528	X-RAY DIFFRACTION	100
2.7041-2.7103	0.1902	432	X-RAY DIFFRACTION	100
2.7103-2.7165	0.1839	538	X-RAY DIFFRACTION	100
2.7165-2.7227	0.1914	504	X-RAY DIFFRACTION	100
2.7227-2.7291	0.1942	516	X-RAY DIFFRACTION	100
2.7291-2.7355	0.1918	412	X-RAY DIFFRACTION	100
2.7355-2.7419	0.1952	568	X-RAY DIFFRACTION	100
2.7419-2.7484	0.2077	442	X-RAY DIFFRACTION	100
2.7484-2.755	0.1883	528	X-RAY DIFFRACTION	100
2.755-2.7616	0.1871	564	X-RAY DIFFRACTION	100
2.7616-2.7683	0.192	492	X-RAY DIFFRACTION	100
2.7683-2.7751	0.1852	488	X-RAY DIFFRACTION	100
2.7751-2.7819	0.1986	516	X-RAY DIFFRACTION	100
2.7819-2.7888	0.1785	524	X-RAY DIFFRACTION	100
2.7888-2.7958	0.1947	516	X-RAY DIFFRACTION	100
2.7958-2.8028	0.1843	546	X-RAY DIFFRACTION	100
2.8028-2.8099	0.1875	478	X-RAY DIFFRACTION	100
2.8099-2.8171	0.1751	439	X-RAY DIFFRACTION	100
2.8171-2.8244	0.1975	560	X-RAY DIFFRACTION	100
2.8244-2.8317	0.2036	490	X-RAY DIFFRACTION	100
2.8317-2.8391	0.1889	499	X-RAY DIFFRACTION	100
2.8391-2.8466	0.1738	460	X-RAY DIFFRACTION	100
2.8466-2.8542	0.1717	500	X-RAY DIFFRACTION	100
2.8542-2.8618	0.1918	468	X-RAY DIFFRACTION	100
2.8618-2.8695	0.1916	618	X-RAY DIFFRACTION	100
2.8695-2.8773	0.1833	480	X-RAY DIFFRACTION	100
2.8773-2.8852	0.2213	532	X-RAY DIFFRACTION	100
2.8852-2.8932	0.2207	500	X-RAY DIFFRACTION	100
2.8932-2.9013	0.2023	540	X-RAY DIFFRACTION	100
2.9013-2.9095	0.1948	451	X-RAY DIFFRACTION	100
2.9095-2.9177	0.2171	527	X-RAY DIFFRACTION	100
2.9177-2.9261	0.2014	524	X-RAY DIFFRACTION	100
2.9261-2.9345	0.1897	392	X-RAY DIFFRACTION	100
2.9345-2.9431	0.1882	540	X-RAY DIFFRACTION	100
2.9431-2.9517	0.1777	568	X-RAY DIFFRACTION	100
2.9517-2.9605	0.206	430	X-RAY DIFFRACTION	100
2.9605-2.9693	0.1886	544	X-RAY DIFFRACTION	100
2.9693-2.9783	0.1886	436	X-RAY DIFFRACTION	100
2.9783-2.9874	0.202	544	X-RAY DIFFRACTION	100
2.9874-2.9966	0.1989	562	X-RAY DIFFRACTION	100
2.9966-3.0059	0.2312	536	X-RAY DIFFRACTION	100
3.0059-3.0153	0.2405	536	X-RAY DIFFRACTION	100
3.0153-3.0248	0.233	442	X-RAY DIFFRACTION	100
3.0248-3.0345	0.2051	524	X-RAY DIFFRACTION	100
3.0345-3.0443	0.1967	476	X-RAY DIFFRACTION	100
3.0443-3.0542	0.201	512	X-RAY DIFFRACTION	100
3.0542-3.0642	0.2083	384	X-RAY DIFFRACTION	100
3.0642-3.0744	0.2213	588	X-RAY DIFFRACTION	100
3.0744-3.0847	0.1979	552	X-RAY DIFFRACTION	100
3.0847-3.0951	0.2145	446	X-RAY DIFFRACTION	100
3.0951-3.1057	0.2073	548	X-RAY DIFFRACTION	100
3.1057-3.1165	0.2395	520	X-RAY DIFFRACTION	100
3.1165-3.1273	0.1961	444	X-RAY DIFFRACTION	100
3.1273-3.1384	0.1978	600	X-RAY DIFFRACTION	100
3.1384-3.1496	0.1846	510	X-RAY DIFFRACTION	100
3.1496-3.1609	0.1654	436	X-RAY DIFFRACTION	100
3.1609-3.1725	0.1722	484	X-RAY DIFFRACTION	100
3.1725-3.1842	0.1858	548	X-RAY DIFFRACTION	100
3.1842-3.196	0.1908	492	X-RAY DIFFRACTION	100
3.196-3.2081	0.1919	456	X-RAY DIFFRACTION	100
3.2081-3.2203	0.1886	560	X-RAY DIFFRACTION	100
3.2203-3.2327	0.2061	528	X-RAY DIFFRACTION	100
3.2327-3.2453	0.1965	478	X-RAY DIFFRACTION	100
3.2453-3.2582	0.2168	592	X-RAY DIFFRACTION	100
3.2582-3.2712	0.2024	442	X-RAY DIFFRACTION	100
3.2712-3.2844	0.1993	534	X-RAY DIFFRACTION	100
3.2844-3.2979	0.1837	430	X-RAY DIFFRACTION	100
3.2979-3.3115	0.1793	508	X-RAY DIFFRACTION	100
3.3115-3.3254	0.1737	552	X-RAY DIFFRACTION	100
3.3254-3.3396	0.1964	428	X-RAY DIFFRACTION	100
3.3396-3.3539	0.186	540	X-RAY DIFFRACTION	100
3.3539-3.3686	0.1731	528	X-RAY DIFFRACTION	100
3.3686-3.3835	0.1767	556	X-RAY DIFFRACTION	100
3.3835-3.3986	0.1591	498	X-RAY DIFFRACTION	100
3.3986-3.414	0.1656	516	X-RAY DIFFRACTION	100
3.414-3.4298	0.1754	452	X-RAY DIFFRACTION	100
3.4298-3.4458	0.1734	496	X-RAY DIFFRACTION	100
3.4458-3.4621	0.1741	484	X-RAY DIFFRACTION	100
3.4621-3.4787	0.1721	502	X-RAY DIFFRACTION	100
3.4787-3.4956	0.1727	536	X-RAY DIFFRACTION	100
3.4956-3.5129	0.1687	472	X-RAY DIFFRACTION	100
3.5129-3.5306	0.1811	524	X-RAY DIFFRACTION	100
3.5306-3.5485	0.2026	516	X-RAY DIFFRACTION	100
3.5485-3.5669	0.1643	582	X-RAY DIFFRACTION	100
3.5669-3.5857	0.1536	466	X-RAY DIFFRACTION	100
3.5857-3.6048	0.1658	460	X-RAY DIFFRACTION	100
3.6048-3.6244	0.1677	504	X-RAY DIFFRACTION	100
3.6244-3.6444	0.1662	468	X-RAY DIFFRACTION	100
3.6444-3.6648	0.1469	574	X-RAY DIFFRACTION	100
3.6648-3.6857	0.1461	448	X-RAY DIFFRACTION	100
3.6857-3.7071	0.1514	564	X-RAY DIFFRACTION	100
3.7071-3.729	0.1802	528	X-RAY DIFFRACTION	100
3.729-3.7514	0.162	456	X-RAY DIFFRACTION	100
3.7514-3.7744	0.126	546	X-RAY DIFFRACTION	100
3.7744-3.798	0.1438	476	X-RAY DIFFRACTION	100
3.798-3.8221	0.1452	482	X-RAY DIFFRACTION	100
3.8221-3.8469	0.138	468	X-RAY DIFFRACTION	100
3.8469-3.8723	0.1329	587	X-RAY DIFFRACTION	100
3.8723-3.8985	0.148	470	X-RAY DIFFRACTION	100
3.8985-3.9253	0.1238	570	X-RAY DIFFRACTION	100
3.9253-3.9529	0.1485	464	X-RAY DIFFRACTION	100
3.9529-3.9813	0.1399	524	X-RAY DIFFRACTION	100
3.9813-4.0105	0.1458	458	X-RAY DIFFRACTION	100
4.0105-4.0406	0.146	456	X-RAY DIFFRACTION	100
4.0406-4.0716	0.1481	570	X-RAY DIFFRACTION	100
4.0716-4.1036	0.1552	528	X-RAY DIFFRACTION	100
4.1036-4.1366	0.147	522	X-RAY DIFFRACTION	100
4.1366-4.1707	0.1465	443	X-RAY DIFFRACTION	100
4.1707-4.206	0.1177	556	X-RAY DIFFRACTION	100
4.206-4.2425	0.1404	456	X-RAY DIFFRACTION	100
4.2425-4.2803	0.1383	522	X-RAY DIFFRACTION	100
4.2803-4.3195	0.1143	524	X-RAY DIFFRACTION	100
4.3195-4.3601	0.1269	554	X-RAY DIFFRACTION	100
4.3601-4.4023	0.144	430	X-RAY DIFFRACTION	100
4.4023-4.4463	0.135	500	X-RAY DIFFRACTION	100
4.4463-4.492	0.1229	508	X-RAY DIFFRACTION	100
4.492-4.5396	0.1208	526	X-RAY DIFFRACTION	100
4.5396-4.5894	0.1294	544	X-RAY DIFFRACTION	100
4.5894-4.6414	0.1222	464	X-RAY DIFFRACTION	100
4.6414-4.6958	0.1381	516	X-RAY DIFFRACTION	100
4.6958-4.7529	0.1391	470	X-RAY DIFFRACTION	100
4.7529-4.8129	0.1212	532	X-RAY DIFFRACTION	100
4.8129-4.876	0.1302	542	X-RAY DIFFRACTION	100
4.876-4.9425	0.1306	538	X-RAY DIFFRACTION	100
4.9425-5.0129	0.1371	400	X-RAY DIFFRACTION	100
5.0129-5.0874	0.1297	510	X-RAY DIFFRACTION	100
5.0874-5.1666	0.1124	544	X-RAY DIFFRACTION	100
5.1666-5.251	0.1428	510	X-RAY DIFFRACTION	100
5.251-5.3411	0.1537	495	X-RAY DIFFRACTION	100
5.3411-5.4378	0.1586	514	X-RAY DIFFRACTION	100
5.4378-5.5418	0.1473	472	X-RAY DIFFRACTION	100
5.5418-5.6544	0.1265	528	X-RAY DIFFRACTION	100
5.6544-5.7766	0.1612	484	X-RAY DIFFRACTION	100
5.7766-5.9102	0.1501	516	X-RAY DIFFRACTION	100
5.9102-6.057	0.1446	530	X-RAY DIFFRACTION	100
6.057-6.2197	0.1549	478	X-RAY DIFFRACTION	100
6.2197-6.4013	0.1664	516	X-RAY DIFFRACTION	100
6.4013-6.6062	0.1625	492	X-RAY DIFFRACTION	100
6.6062-6.8401	0.1462	526	X-RAY DIFFRACTION	100
6.8401-7.1111	0.153	504	X-RAY DIFFRACTION	100
7.1111-7.431	0.1565	494	X-RAY DIFFRACTION	100
7.431-7.8174	0.1697	514	X-RAY DIFFRACTION	100
7.8174-8.2993	0.1488	490	X-RAY DIFFRACTION	100
8.2993-8.9273	0.1497	511	X-RAY DIFFRACTION	99
8.9273-9.8024	0.121	516	X-RAY DIFFRACTION	99
9.8024-11.1683	0.1586	496	X-RAY DIFFRACTION	97
11.1683-13.8793	0.174	475	X-RAY DIFFRACTION	97
13.8793-32.1152	0.3306	465	X-RAY DIFFRACTION	93

-
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

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 5 types, 393 molecules

-
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, 6 molecules ABCDEF

-Non-polymers , 5 types, 393 molecules

-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, 6 molecules ABCDEF

-
Non-polymers , 5 types, 393 molecules

-
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