PDB-5iqa: Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH...

ID or keywords:

Entry

Database: PDB / ID: 5iqa

Title

Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPNP and Magnesium

Components

Bifunctional AAC/APH

Keywords

TRANSFERASE /

Kinase /

Antibiotic /

Aminoglycoside / Resistance

Function / homology

Function and homology information

aminoglycoside phosphotransferase activity / aminoglycoside 2''-phosphotransferase / acyltransferase activity, transferring groups other than amino-acyl groups /

Transferases; Acyltransferases; Transferring groups other than aminoacyl groups /

phosphorylation / response to antibiotic /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Caldwell, S.J. / Berghuis, A.M.

Funding support

Canada, 1items

Citation

Journal: Structure / Year: 2016
Title: Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia.
Authors: Caldwell, S.J. / Huang, Y. / Berghuis, A.M.

History

Deposition	Mar 10, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 15, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5iqa.cif.gz	529.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5iqa.ent.gz	435.5 KB	Display	PDB format
PDBx/mmJSON format	5iqa.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqa ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqa	HTTPS FTP

-
Related structure data

Related structure data	5bylC 5iqbC 5iqcC 5iqdC 5iqeC 5iqfC 5iqgC 5iqhC 5iqiC 3uzrS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5iqc-3 6ch4-1 5iqi-1 5iqb-4 6cav-4 5iqh-1 6cgg-3 5iqf-2 5iqb-2 6c5u-2 5iqd-2 6cav-1 6cgg-2 5iqf-4 6cgg-4 5iqb-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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (5) #97 - Jan 2008 Circadian Clock Proteins similarity (3) #148 - Apr 2012 Ras Protein similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Bifunctional AAC/APH

B: Bifunctional AAC/APH

C: Bifunctional AAC/APH

D: Bifunctional AAC/APH

hetero molecules

146 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bifunctional AAC/APH

hetero molecules

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

2

B: Bifunctional AAC/APH

hetero molecules

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

3

C: Bifunctional AAC/APH

hetero molecules

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

4

D: Bifunctional AAC/APH

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.170, 100.320, 94.060
Angle α, β, γ (deg.)	90.00, 105.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-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
1	1	ASN	ASN	LYS	LYS	A	A	182 - 478	8 - 304
2	1	ASN	ASN	LYS	LYS	B	B	182 - 478	8 - 304
1	2	ASN	ASN	ASP	ASP	A	A	182 - 479	8 - 305
2	2	ASN	ASN	ASP	ASP	C	C	182 - 479	8 - 305
1	3	ASN	ASN	LYS	LYS	A	A	182 - 478	8 - 304
2	3	ASN	ASN	LYS	LYS	D	D	182 - 478	8 - 304
1	4	ASN	ASN	LYS	LYS	B	B	182 - 478	8 - 304
2	4	ASN	ASN	LYS	LYS	C	C	182 - 478	8 - 304
1	5	TYR	TYR	ASP	ASP	B	B	179 - 479	5 - 305
2	5	TYR	TYR	ASP	ASP	D	D	179 - 479	5 - 305
1	6	ASN	ASN	LYS	LYS	C	C	182 - 478	8 - 304
2	6	ASN	ASN	LYS	LYS	D	D	182 - 478	8 - 304

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Bifunctional AAC/APH Mass: 35948.199 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 175-479) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aacA-aphD, R015, VRA0030 / Plasmid: pET-22b-APH(2'')-Ia / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(LDE3) References: UniProt: P0A0C1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical	ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₃P₃ Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.87 Å³/Da / Density % sol: 57.13 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 80-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: May 5, 2013
Radiation	Monochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.15→56.04 Å / Num. obs: 83016 / % possible obs: 94.4 % / Redundancy: 4.7 % / R_merge(I) obs: 0.108 / Net I/σ(I): 7.8
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 4.6 % / R_merge(I) obs: 1.211 / Mean I/σ(I) obs: 1.4 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
MOSFLM	0.1.27	data reduction
Aimless	0.3.11	data scaling
PHASER	2.5.1	phasing
Coot	0.7.2	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3UZR

3uzr

Resolution: 2.15→56.04 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.955 / SU B: 10.798 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20567	4160	5 %	RANDOM
R_work	0.16687	-	-	-
obs	0.16882	78819	94.31 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 50.352 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	-0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→56.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9813	0	139	721	10673

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	10170
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	9266
X-RAY DIFFRACTION	r_angle_refined_deg	1.562	1.968	13772
X-RAY DIFFRACTION	r_angle_other_deg	1.289	3	21400
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.714	5	1194
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.258	25.604	546
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.707	15	1835
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.18	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1492
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	11720
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2307
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.802	3.091	4776
X-RAY DIFFRACTION	r_mcbond_other	2.802	3.09	4775
X-RAY DIFFRACTION	r_mcangle_it	4.125	4.611	5961
X-RAY DIFFRACTION	r_mcangle_other	4.125	4.612	5962
X-RAY DIFFRACTION	r_scbond_it	3.988	3.496	5394
X-RAY DIFFRACTION	r_scbond_other	3.988	3.496	5394
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.268	5.074	7809
X-RAY DIFFRACTION	r_long_range_B_refined	8.839	25.924	12208
X-RAY DIFFRACTION	r_long_range_B_other	8.84	25.872	12180
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	17745	0.1
1	2	B	17745	0.1
2	1	A	17882	0.09
2	2	C	17882	0.09
3	1	A	17682	0.1
3	2	D	17682	0.1
4	1	B	17663	0.1
4	2	C	17663	0.1
5	1	B	18106	0.08
5	2	D	18106	0.08
6	1	C	17616	0.1
6	2	D	17616	0.1

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.287	305	-
R_work	0.291	6131	-
obs	-	-	99.98 %

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	2.5491	4.3113	1.8205	8.4443	1.804	2.7277	0.0094	0.0648	0.1347	-0.3244	0.1764	0.4778	0.3472	-0.0205	-0.1858	0.2425	0.0332	-0.0211	0.3153	0.0196	0.0933	46.558	-2.864	55.901
2	7.7409	1.8903	-4.7174	8.361	-2.2497	7.2158	0.0227	0.0004	0.0524	-0.1718	0.0251	0.5899	0.1922	-0.2112	-0.0478	0.0655	-0.0173	-0.0228	0.0964	-0.0085	0.1022	44.745	-2.563	36.67
3	1.2058	0.0854	0.8409	2.0253	-0.9831	4.8528	0.0587	0.0826	0.1636	-0.2759	-0.2354	-0.1907	0.1481	0.5246	0.1768	0.0615	0.0416	0.0503	0.2869	0.0287	0.0531	54.814	2.485	51.557
4	8.61	-2.1945	-8.9793	17.8922	4.6808	9.7104	0.0847	0.6336	0.1216	0.1201	-0.0862	0.7553	-0.0151	-0.6719	0.0015	0.2376	0.0106	0.0137	0.3262	-0.0195	0.1658	41.683	0.127	49.988
5	6.9187	-3.1875	3.6465	1.7346	-0.4103	8.1796	0.0624	0.0842	0.2469	-0.1266	-0.1725	-0.135	-0.2967	-0.5451	0.1101	0.2599	-0.0261	0.0726	0.1958	-0.0558	0.3025	43.004	14.047	53.035
6	2.4324	-0.9191	0.0969	3.1105	-1.0092	1.7793	0.0764	0.0213	-0.1063	-0.0605	-0.0463	0.1422	0.0121	-0.0169	-0.03	0.0339	-0.027	0.0027	0.1155	-0.0063	0.0304	46.002	-6.012	71.176
7	3.1043	-1.7544	0.5789	1.7804	-0.4348	0.975	-0.002	-0.0886	0.1679	0.1535	0.0013	0.0934	-0.2344	-0.0013	0.0006	0.1038	-0.0016	0.0565	0.0913	0.0049	0.1281	29.052	11.177	71.359
8	7.7376	3.9159	-2.9344	7.5759	-2.8766	4.7847	-0.1086	0.3399	-0.4874	-0.4782	-0.0522	-0.3584	0.1551	-0.0591	0.1609	0.0999	0.0551	0.0589	0.1258	-0.0219	0.0773	24.35	6.303	59.285
9	14.8089	-11.4793	-0.4783	9.7411	-1.5724	6.3928	-0.2434	-1.0138	-0.4274	0.1678	0.5056	0.3164	-0.3584	-0.0656	-0.2621	0.3241	0.1141	0.0034	0.5162	0.097	0.2486	36.895	4.56	20.788
10	4.9848	1.4425	-1.623	6.4527	-1.5477	0.7224	0.1108	-0.2152	-0.1874	-0.035	-0.1123	0.271	-0.0327	0.0714	0.0016	0.121	-0.0138	-0.0157	0.1013	0.0262	0.0339	37.666	2.664	41.156
11	1.3464	0.296	0.7508	1.4918	-0.452	6.1384	-0.1394	-0.197	0.2238	0.1448	-0.006	-0.076	-0.6651	-0.0292	0.1453	0.2714	0.0984	0.0092	0.0736	-0.011	0.0651	43.044	12.922	24.022
12	8.9573	-8.7605	-8.1675	20.0163	6.876	7.8591	-0.2099	0.2719	-0.6038	0.095	-0.0981	0.6479	0.3312	-0.2542	0.308	0.3387	0.0116	0.0191	0.2424	-0.0087	0.2672	39.69	0.229	27.182
13	4.5984	-5.6409	5.4436	7.5364	-3.9568	19.3542	-0.1509	0.0885	0.1923	0.1094	-0.0645	-0.2962	-0.537	0.5222	0.2153	0.0504	-0.0418	0.0064	0.1216	0.0121	0.13	54.815	1.785	23.452
14	3.3978	-1.337	0.9771	2.5944	-0.2298	1.1983	-0.1841	-0.046	-0.0948	0.0609	0.2118	0.2466	-0.0768	-0.0891	-0.0278	0.0948	0.0288	0.0022	0.0829	0.0508	0.0831	33.671	2.712	5.676
15	1.3584	-1.2314	0.476	2.9896	-0.7095	0.6699	-0.0019	0.0744	-0.0662	-0.0588	-0.07	-0.0528	-0.018	-0.0321	0.0718	0.0511	0.0002	0.0277	0.0713	-0.0321	0.1006	49.822	-15.327	7.771
16	4.1647	2.4716	2.1377	7.4335	1.6334	3.2534	0.007	-0.3398	0.3012	0.4189	-0.1144	0.686	-0.1661	-0.2737	0.1073	0.1225	0.0196	0.0822	0.1154	-0.0412	0.1106	44.316	-18.8	20.148
17	0.4815	-1.5316	-1.0324	16.936	1.3602	2.5273	0.0573	0.0748	0.0416	-0.8202	-0.0055	-0.5503	-0.0141	-0.223	-0.0518	0.1483	0.0323	0.0019	0.322	-0.0143	0.2109	64.314	35.714	75.249
18	11.8495	1.9707	10.6453	6.8463	6.7922	14.2715	-0.0161	0.1719	0.1681	-0.5816	0.0819	-0.6469	-0.5174	0.2694	-0.0659	0.0989	-0.0319	0.0469	0.1229	0.0264	0.2805	66.301	35.06	56.069
19	2.1553	-0.5	0.2182	1.7819	1.5	5.8732	-0.064	0.1186	-0.0116	-0.3162	-0.1283	0.1198	0.0493	-0.5526	0.1922	0.0985	-0.0223	-0.0271	0.1968	-0.0659	0.1856	56.119	30.302	70.994
20	14.2262	-10.9878	2.3845	18.2617	1.4209	8.7065	0.4563	0.0247	0.2005	0.3723	-0.3694	-0.7147	-0.2597	0.7138	-0.087	0.1173	-0.0736	-0.0451	0.2358	0.0296	0.2166	69.233	32.448	69.548
21	0.2175	-0.5306	1.0334	2.1307	-0.7534	8.7501	0.0586	0.1108	0.0593	-0.1516	-0.3751	-0.0648	0.4012	0.2379	0.3165	0.3975	-0.0173	0.0117	0.3558	0.0292	0.4015	68.696	18.547	73.078
22	1.8844	-1.1766	0.6443	2.3749	-1.3918	2.9652	-0.1709	-0.1218	0.2125	0.1453	-0.0464	-0.0557	-0.2851	-0.22	0.2173	0.0436	0.0516	-0.0724	0.1305	-0.1058	0.2363	64.44	39.506	90.342
23	2.3189	-1.0104	-0.4955	1.9225	0.4648	1.3722	-0.1735	-0.0556	-0.2603	0.0146	0.0319	0.182	0.1369	-0.0953	0.1416	0.0318	-0.0081	0.045	0.0573	-0.0064	0.1259	81.898	22.402	92.009
24	6.6324	2.3064	1.4169	5.4816	2.3125	6.526	-0.2137	0.2314	0.2894	-0.2319	0.0133	0.4125	0.0848	-0.3287	0.2005	0.0492	0.0031	-0.0061	0.1145	-0.0255	0.0609	86.843	26.519	79.898
25	12.4916	-5.2895	-7.2268	3.372	3.561	4.4158	-0.3858	-0.676	-0.0917	0.1037	0.311	0.2114	0.1796	0.3779	0.0748	0.1901	0.0334	0.0375	0.2746	0.0676	0.2654	74.502	28.93	40.823
26	9.5071	4.5589	1.2993	16.8401	3.3223	0.7092	0.1439	-0.6693	0.3928	-0.1922	-0.173	-0.2285	-0.0054	-0.0554	0.0292	0.0627	-0.0152	0.0366	0.1355	-0.019	0.111	73.309	29.948	60.951
27	0.3545	0.182	-1.0693	2.4241	-1.3047	6.0395	-0.0898	-0.1026	-0.173	-0.0948	-0.1246	-0.0039	0.169	-0.1824	0.2144	0.1133	0.0166	0.0122	0.287	0.0062	0.2352	68.461	20.22	43.483
28	34.8159	-3.7226	-3.0711	1.4264	3.1398	11.5441	-0.3273	0.3848	2.2214	-0.3461	-0.2087	-0.3346	-0.9878	-0.2588	0.5359	0.4806	-0.0003	-0.0463	0.4249	0.1197	0.4421	71.324	32.788	47.157
29	0.7519	-1.1514	-1.6828	11.232	0.2807	10.2914	-0.3637	-0.0937	0.0096	0.0904	-0.0837	0.3312	-0.113	-0.1903	0.4475	0.3905	0.1056	-0.0977	0.1896	-0.0617	0.1519	56.383	31.48	43.894
30	3.6834	-0.2438	-0.2061	1.9202	-0.8721	1.6293	-0.0485	0.1382	-0.1982	-0.2651	-0.0329	-0.1377	0.1698	0.1212	0.0813	0.0818	-0.0145	0.0831	0.1905	-0.046	0.1294	77.965	31.798	25.882
31	4.2429	-3.4709	-0.0836	3.9798	0.2211	0.4051	-0.1884	0.0906	0.4329	0.2275	0.1427	-0.2953	-0.0734	-0.0169	0.0457	0.0755	-0.0289	-0.06	0.196	0.0343	0.1368	61.346	49.268	28.421
32	11.3577	5.9574	-4.1021	8.9037	-3.1905	9.7755	-0.9612	-1.0335	0.2745	1.2727	0.4009	-1.2412	0.6881	1.1872	0.5603	0.6902	0.403	-0.4299	0.7056	-0.1124	0.3828	66.937	52.667	40.616

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	500
2	X-RAY DIFFRACTION	1	A	700 - 702
3	X-RAY DIFFRACTION	1	A	900 - 906
4	X-RAY DIFFRACTION	2	A	182 - 187
5	X-RAY DIFFRACTION	3	A	188 - 207
6	X-RAY DIFFRACTION	3	A	217 - 229
7	X-RAY DIFFRACTION	3	A	237 - 277
8	X-RAY DIFFRACTION	4	A	208 - 216
9	X-RAY DIFFRACTION	5	A	230 - 236
10	X-RAY DIFFRACTION	6	A	278 - 318
11	X-RAY DIFFRACTION	6	A	367 - 431
12	X-RAY DIFFRACTION	7	A	319 - 366
13	X-RAY DIFFRACTION	7	A	432 - 447
14	X-RAY DIFFRACTION	8	A	448 - 479
15	X-RAY DIFFRACTION	9	B	500
16	X-RAY DIFFRACTION	9	B	700 - 702
17	X-RAY DIFFRACTION	9	B	900 - 909
18	X-RAY DIFFRACTION	10	B	179 - 187
19	X-RAY DIFFRACTION	11	B	188 - 207
20	X-RAY DIFFRACTION	11	B	217 - 229
21	X-RAY DIFFRACTION	11	B	237 - 277
22	X-RAY DIFFRACTION	12	B	208 - 216
23	X-RAY DIFFRACTION	13	B	230 - 236
24	X-RAY DIFFRACTION	14	B	278 - 318
25	X-RAY DIFFRACTION	14	B	367 - 431
26	X-RAY DIFFRACTION	15	B	319 - 366
27	X-RAY DIFFRACTION	15	B	432 - 447
28	X-RAY DIFFRACTION	16	B	448 - 479
29	X-RAY DIFFRACTION	17	C	500
30	X-RAY DIFFRACTION	17	C	700 - 702
31	X-RAY DIFFRACTION	17	C	900 - 906
32	X-RAY DIFFRACTION	18	C	182 - 187
33	X-RAY DIFFRACTION	19	C	188 - 207
34	X-RAY DIFFRACTION	19	C	217 - 229
35	X-RAY DIFFRACTION	19	C	237 - 277
36	X-RAY DIFFRACTION	20	C	208 - 216
37	X-RAY DIFFRACTION	21	C	230 - 236
38	X-RAY DIFFRACTION	22	C	278 - 318
39	X-RAY DIFFRACTION	22	C	367 - 431
40	X-RAY DIFFRACTION	23	C	319 - 366
41	X-RAY DIFFRACTION	23	C	432 - 447
42	X-RAY DIFFRACTION	24	C	448 - 479
43	X-RAY DIFFRACTION	25	D	500
44	X-RAY DIFFRACTION	25	D	700 - 702
45	X-RAY DIFFRACTION	25	D	900 - 911
46	X-RAY DIFFRACTION	26	D	179 - 187
47	X-RAY DIFFRACTION	27	D	188 - 207
48	X-RAY DIFFRACTION	27	D	217 - 229
49	X-RAY DIFFRACTION	27	D	237 - 277
50	X-RAY DIFFRACTION	28	D	208 - 216
51	X-RAY DIFFRACTION	29	D	230 - 236
52	X-RAY DIFFRACTION	30	D	278 - 318
53	X-RAY DIFFRACTION	30	D	367 - 431
54	X-RAY DIFFRACTION	31	D	319 - 366
55	X-RAY DIFFRACTION	31	D	432 - 447
56	X-RAY DIFFRACTION	32	D	448 - 479

-
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