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

ID or keywords:

Entry

Database: PDB / ID: 5iqf

Title

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

Components

Bifunctional AAC/APH

Keywords

TRANSFERASE / Kinase / Antibiotic / Aminoglycoside / Resistance

Function / homology

Function and homology information

aminoglycoside phosphotransferase activity / aminoglycoside 2''-phosphotransferase / N-acyltransferase activity / 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 /

FOURIER SYNTHESIS / Resolution: 2.35 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_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_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.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	5iqf.cif.gz	534.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5iqf.ent.gz	439.6 KB	Display	PDB format
PDBx/mmJSON format	5iqf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5iqf_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5iqf_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5iqf_validation.xml.gz	53.8 KB	Display
Data in CIF	5iqf_validation.cif.gz	77.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqf ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqf	HTTPS FTP

-
Related structure data

Related structure data	5bylSC 5iqaC 5iqbC 5iqcC 5iqdC 5iqeC 5iqgC 5iqhC 5iqiC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5iqd-3 5iqg-1 6ch4-4 6ch4-3 4ork-3 5iqe-1 3n4v-2 5iqh-1 5iqe-3 5iqb-3 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

5bylSC

S: Starting model for refinement

C: citing same article (ref.)

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)

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

2

B: Bifunctional AAC/APH

hetero molecules

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

3

C: Bifunctional AAC/APH

hetero molecules

defined by author
36.5 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)	90.454, 99.075, 92.350
Angle α, β, γ (deg.)	90.00, 105.18, 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: _ / Refine code: _

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	TYR	TYR	A	A	182 - 477	8 - 303
2	2	ASN	ASN	TYR	TYR	C	C	182 - 477	8 - 303
1	3	ASN	ASN	TYR	TYR	A	A	182 - 477	8 - 303
2	3	ASN	ASN	TYR	TYR	D	D	182 - 477	8 - 303
1	4	TYR	TYR	TYR	TYR	B	B	179 - 477	5 - 303
2	4	TYR	TYR	TYR	TYR	C	C	179 - 477	5 - 303
1	5	TYR	TYR	LYS	LYS	B	B	179 - 478	5 - 304
2	5	TYR	TYR	LYS	LYS	D	D	179 - 478	5 - 304
1	6	ARG	ARG	LYS	LYS	C	C	178 - 478	4 - 304
2	6	ARG	ARG	LYS	LYS	D	D	178 - 478	4 - 304

NCS ensembles :

ID
1
2
3
4
5
6

-
Protein , 1 types, 4 molecules ABCD

#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 (E. coli) / 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

#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 (E. coli) / 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

-
Non-polymers , 5 types, 937 molecules

#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*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 Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.78 Å³/Da / Density % sol: 55.71 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.35→89.13 Å / Num. obs: 65601 / % possible obs: 100 % / Redundancy: 7.2 % / B_iso Wilson estimate: 35.1 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.139 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.35→2.41 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.211 / Mean I/σ(I) obs: 1.7 / % possible all: 100

-
Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5BYL

5byl

Resolution: 2.35→89.13 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22783	3318	5.1 %	RANDOM
R_work	0.18001	-	-	-
obs	0.18244	62255	99.94 %	-

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: 49.218 Å²

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

Refinement step

Cycle: LAST / Resolution: 2.35→89.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9817	0	129	921	10867

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.02	10159
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	9280
X-RAY DIFFRACTION	r_angle_refined_deg	1.537	1.977	13743
X-RAY DIFFRACTION	r_angle_other_deg	3.606	3	21435
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.523	5	1198
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.872	25.655	550
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.169	15	1837
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.933	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1496
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	11489
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	2317
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	1.638	2.524	4780
X-RAY DIFFRACTION	r_mcbond_other	1.637	2.523	4779
X-RAY DIFFRACTION	r_mcangle_it	2.53	3.777	5967
X-RAY DIFFRACTION	r_mcangle_other	2.53	3.777	5968
X-RAY DIFFRACTION	r_scbond_it	2.404	2.768	5379
X-RAY DIFFRACTION	r_scbond_other	2.404	2.768	5379
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.801	4.055	7772
X-RAY DIFFRACTION	r_long_range_B_refined	7.691	21.906	12893
X-RAY DIFFRACTION	r_long_range_B_other	7.658	21.751	12810
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	18018	0.1
1	2	B	18018	0.1
2	1	A	17931	0.09
2	2	C	17931	0.09
3	1	A	17714	0.11
3	2	D	17714	0.11
4	1	B	17923	0.11
4	2	C	17923	0.11
5	1	B	18428	0.09
5	2	D	18428	0.09
6	1	C	17862	0.12
6	2	D	17862	0.12

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	265	-
R_work	0.288	4546	-
obs	-	-	99.9 %

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	0.6128	-0.8135	1.2171	1.0958	-1.6328	2.4372	0.1471	0.0513	-0.0136	-0.2562	-0.0664	0.0569	0.3472	0.1098	-0.0807	0.3629	-0.0067	-0.0533	0.3433	0.004	0.2036	46.799	-2.562	54.587
2	0.4555	0.1732	0.4111	0.0743	0.1635	0.3832	-0.0507	0.078	-0.0908	-0.0393	0.0565	0.0195	-0.0324	0.0594	-0.0058	0.5065	-0.0113	0.0571	0.4617	0.005	0.5137	45.137	-3.432	35.924
3	3.1025	-0.6222	1.6201	4.4925	-1.8384	7.3591	0.2532	0.2634	0.12	-0.6825	-0.5621	-0.4015	0.0035	0.8494	0.3089	0.1453	0.0653	0.0447	0.4851	0.0973	0.1736	55.286	3.183	50.668
4	8.3911	3.0705	1.5454	1.1665	0.1118	5.085	0.2083	-0.0405	0.2823	0.0701	0.0013	0.128	0.0598	-0.2023	-0.2095	0.3539	0.0255	-0.0125	0.2736	0.0293	0.2233	43.926	-0.119	49.078
5	16.4419	-5.1361	11.5365	1.6069	-3.6033	8.0961	-0.3014	0.0186	0.4642	0.082	-0.0302	-0.1268	-0.1917	-0.0015	0.3317	0.405	-0.021	-0.0159	0.3714	-0.0593	0.448	43.028	14.399	52.302
6	3.3196	-2.1646	-0.0473	6.4598	-1.2976	3.3195	-0.0111	0.0745	-0.1729	0.0181	-0.1637	0.3797	0.0061	-0.0064	0.1748	0.0098	-0.0432	-0.0055	0.2153	0.0057	0.0569	45.739	-5.978	69.601
7	4.5782	-2.378	0.6911	3.6799	-0.4232	2.3496	-0.1228	-0.0254	0.1651	0.4255	0.0158	0.0776	-0.3908	0.264	0.107	0.1581	-0.0629	0.0823	0.0953	-0.0377	0.1596	28.701	10.987	69.487
8	10.1884	3.505	-2.3261	6.9193	-1.4028	5.8254	-0.2849	0.3197	-0.4032	-0.4522	0.087	-0.281	0.0823	0.2523	0.1979	0.1029	0.0296	0.0465	0.2262	-0.0683	0.1664	24.262	6.039	57.399
9	4.5885	0.7546	-1.0261	0.4163	-0.5876	0.8331	0.0871	-0.624	-0.1519	-0.0954	-0.1173	-0.0296	0.1126	0.1592	0.0302	0.3175	0.0266	-0.0309	0.3461	-0.0285	0.1834	37.471	4.504	20.328
10	8.4852	6.9096	-3.7585	5.6711	-3.0848	1.6868	-0.0434	-0.0213	-0.0033	-0.1017	0.0505	0.0886	0.0954	-0.0468	-0.0071	0.4348	-0.0171	0.0063	0.3404	-0.0009	0.3888	38.26	2.654	41.087
11	2.562	-0.2366	0.6712	2.0434	-0.5725	8.5206	-0.1453	-0.2362	0.2785	0.0609	0.0136	-0.1012	-0.6284	0.402	0.1316	0.3982	0.0061	-0.0802	0.1305	-0.0095	0.2599	43.672	12.882	23.263
12	3.13	2.4579	2.4112	12.6385	-3.0896	4.1932	0.1487	-0.2656	-0.3352	0.0863	0.0993	-0.1077	0.12	-0.3239	-0.2481	0.3477	0.0362	-0.054	0.2881	0.0497	0.4912	39.604	1.187	24.895
13	1.632	-1.8183	-0.5543	6.9931	-8.3203	16.2719	-0.193	-0.0036	0.1523	0.0351	-0.1837	-0.4037	0.3737	0.3242	0.3767	0.3691	0.0403	-0.1062	0.3281	-0.0137	0.3619	51.443	-1.802	22.672
14	6.6111	-1.3095	-0.7589	2.8057	0.2526	3.035	-0.0987	0.1414	-0.1871	-0.0964	0.0176	0.2498	0.0031	-0.1191	0.0811	0.2463	0.0169	-0.0634	0.0518	0.0526	0.1207	33.926	2.604	5.424
15	3.0681	-1.547	0.3925	5.2373	-1.2815	1.4965	0.0068	0.3158	-0.0391	-0.0876	-0.095	0.0286	-0.159	0.0333	0.0883	0.1019	-0.0222	0.053	0.0899	-0.0492	0.0856	49.92	-15.129	7.643
16	7.6568	4.1345	4.3719	11.9381	3.3354	8.8518	0.1673	-0.5998	0.3544	0.857	-0.4086	0.56	-0.0595	-0.5101	0.2414	0.1811	0.0224	0.1384	0.1039	-0.026	0.1619	44.581	-18.211	20.369
17	9.0768	-8.9131	1.4084	12.286	2.616	4.7859	0.497	0.0063	-0.0517	-1.0681	-0.2199	-0.2431	-0.4931	-0.2643	-0.2771	0.3404	-0.0668	0.1424	0.2265	-0.012	0.1625	64.535	34.617	73.919
18	10.6637	2.1094	-3.6226	0.711	0.3252	4.9506	0.8745	-0.1016	2.3803	-0.272	0.2215	0.3956	-1.7918	0.9126	-1.0961	1.0319	-0.2771	0.2358	0.3855	-0.0586	0.6423	66.275	35.588	56.08
19	1.7717	0.2492	0.4019	1.2958	0.546	7.7735	0.1213	-0.1454	-0.0605	-0.1432	-0.1887	0.1636	0.1431	-0.624	0.0675	0.0753	-0.0838	-0.0233	0.2999	-0.0023	0.155	56.251	28.488	70.173
20	4.7877	2.9924	-0.8858	2.0773	0.481	5.3443	-0.0905	0.1908	-0.2294	-0.0142	0.1672	-0.1762	0.255	0.1869	-0.0767	0.2448	-0.0489	0.0338	0.2411	-0.0361	0.2646	68.234	32.39	68.657
21	13.224	-10.1084	-11.5628	7.7316	8.8447	10.1187	-0.5112	-0.1017	-0.4994	0.4246	0.1005	0.3534	0.5026	0.117	0.4108	0.5779	-0.0105	-0.0125	0.5755	0.0964	0.5527	69.452	18.622	72.146
22	3.1606	-1.1367	0.4822	3.9597	-1.3242	4.6857	-0.0884	-0.0855	0.3086	0.0256	0.0244	-0.1169	-0.3137	-0.354	0.064	0.0281	-0.0041	-0.004	0.2843	-0.0367	0.0511	64.995	38.567	88.833
23	5.8171	-1.7316	-2.3513	1.6635	0.441	2.6481	-0.3395	-0.1294	-0.5354	0.001	0.0926	0.0203	0.4531	-0.1888	0.2468	0.1116	-0.0271	0.0545	0.0587	0.0327	0.1028	82.753	21.991	90.336
24	10.1025	3.155	1.0302	9.5633	0.0647	7.9025	-0.3787	0.4096	0.2642	-0.4942	0.0397	0.6795	0.1429	-0.5098	0.3391	0.1211	-0.0017	0.0384	0.1488	0.005	0.1152	87.431	25.956	78.037
25	0.5638	2.2334	-0.0838	8.8941	-0.2843	0.0616	0.0105	-0.0039	-0.1119	0.1537	0.0006	-0.4689	0.112	0.0249	-0.0112	0.2824	0.0326	-0.0188	0.2566	-0.0021	0.1738	74.96	29.46	40.277
26	5.0431	7.0678	4.0962	11.0748	6.4435	3.7535	0.2334	-0.2076	-0.0148	0.0819	0.0127	-0.449	0.0141	0.0167	-0.2461	0.3152	-0.0113	-0.022	0.3482	-0.0041	0.326	73.585	30.452	60.58
27	2.1404	0.4077	-0.4569	1.8081	-0.2951	6.9679	-0.17	-0.0679	-0.5157	-0.0507	0.049	-0.0803	0.5384	0.054	0.1211	0.0613	-0.0026	0.041	0.1648	-0.0014	0.2484	69.019	20.692	42.794
28	10.9522	-0.6529	-6.5165	6.7558	1.7815	4.2639	-0.023	-0.1234	0.22	0.0822	0.1648	-0.6638	-0.11	0.1986	-0.1418	0.2226	-0.1421	-0.1903	0.2865	-0.0036	0.2833	72.762	32.418	44.842
29	5.6728	-1.6831	1.0731	0.5112	-0.3241	0.2105	0.0985	0.1112	0.0167	-0.0791	-0.0532	0.0365	0.025	-0.0032	-0.0454	0.4037	0.0711	-0.0242	0.422	0.0812	0.3301	59.714	35.479	39.299
30	6.2682	-0.7011	0.4466	2.0904	-0.955	2.3365	-0.0562	0.2334	0.0364	-0.0989	-0.0372	-0.2319	0.0581	0.2427	0.0934	0.0541	-0.0292	0.0591	0.2689	-0.0893	0.0907	78.737	31.922	25.582
31	3.967	-2.0393	-1.0594	4.3968	0.4769	1.7782	-0.0425	0.3703	0.503	0.0921	0.081	0.0072	-0.1722	0.0283	-0.0386	0.0521	-0.074	-0.0237	0.2337	0.0533	0.1583	62.045	48.908	28.374
32	6.0114	3.4386	-3.5021	10.2141	-4.2714	8.3274	-0.0461	-0.147	0.4699	0.7351	-0.2171	-0.3699	-0.5815	0.5732	0.2631	0.2264	0.0121	-0.0965	0.3009	-0.0745	0.2588	67.224	51.527	41.21

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 - 906
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 - 478
29	X-RAY DIFFRACTION	17	C	500
30	X-RAY DIFFRACTION	17	C	700 - 702
31	X-RAY DIFFRACTION	17	C	900 - 909
32	X-RAY DIFFRACTION	18	C	177 - 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 - 478
43	X-RAY DIFFRACTION	25	D	500
44	X-RAY DIFFRACTION	25	D	700 - 702
45	X-RAY DIFFRACTION	25	D	900 - 909
46	X-RAY DIFFRACTION	26	D	178 - 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 - 478

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 937 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, 4 molecules ABCD

-Non-polymers , 5 types, 937 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, 4 molecules ABCD

-
Non-polymers , 5 types, 937 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