PDB-5cb6: Structure of adenosine-5'-phosphosulfate kinase

ID or keywords:

Entry

Database: PDB / ID: 5cb6

Title

Structure of adenosine-5'-phosphosulfate kinase

Components

Probable adenylyl-sulfate kinase

Keywords

TRANSFERASE / Synechocystis / sulfur metabolism / enzyme / kinase

Function / homology

Function and homology information

sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / phosphorylation / ATP binding
Similarity search - Function

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.79 Å

Authors

Herrmann, J. / Jez, J.M.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase from Cyanobacteria to Plants.
Authors: Herrmann, J. / Nathin, D. / Lee, S.G. / Sun, T. / Jez, J.M.

History

Deposition	Jun 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	Group: Database references
Revision 1.2	Oct 21, 2015	Group: Database references
Revision 1.3	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 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5cb6.cif.gz	436.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5cb6.ent.gz	360.1 KB	Display	PDB format
PDBx/mmJSON format	5cb6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5cb6_validation.pdf.gz	4.2 MB	Display	wwPDB validaton report
Full document	5cb6_full_validation.pdf.gz	4.2 MB	Display
Data in XML	5cb6_validation.xml.gz	43.2 KB	Display
Data in CIF	5cb6_validation.cif.gz	55.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cb/5cb6 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/5cb6	HTTPS FTP

-
Related structure data

Related structure data	5cb8C 4fxpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cb8-d 2bwj-2 4bs6-d 4dtd-d 4r7q-d 4e1c-d 4gqk-d 3lxs-d 4e1f-d 4dtl-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) 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

5cb8C

4fxpS

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	#116 - Aug 2009 Sulfotransferases similarity (4) #133 - Jan 2011 Nitric Oxide Synthase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#116 - Aug 2009
Sulfotransferases
similarity (4)
#133 - Jan 2011
Nitric Oxide Synthase
similarity (1)
#203 - Nov 2016
Aminopeptidase 1 and Autophagy
similarity (1)
#75 - Mar 2006
Tissue Factor
similarity (1)
#90 - Jun 2007
Fatty Acid Synthase
similarity (1)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Probable adenylyl-sulfate kinase

B: Probable adenylyl-sulfate kinase

C: Probable adenylyl-sulfate kinase

D: Probable adenylyl-sulfate kinase

E: Probable adenylyl-sulfate kinase

F: Probable adenylyl-sulfate kinase

hetero molecules

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

1

A: Probable adenylyl-sulfate kinase

D: Probable adenylyl-sulfate kinase

hetero molecules

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

2

B: Probable adenylyl-sulfate kinase

F: Probable adenylyl-sulfate kinase

hetero molecules

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

3

C: Probable adenylyl-sulfate kinase

hetero molecules

C: Probable adenylyl-sulfate kinase

hetero molecules

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

4

E: Probable adenylyl-sulfate kinase

hetero molecules

E: Probable adenylyl-sulfate kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	136.904, 109.681, 100.807
Angle α, β, γ (deg.)	90.00, 90.72, 90.00
Int Tables number	5
Space group name H-M	C121

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Probable adenylyl-sulfate kinase / APS kinase / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate kinase Mass: 21872.799 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / Gene: cysC, slr0676 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P72940, adenylyl-sulfate kinase

#1: Protein

Probable adenylyl-sulfate kinase / APS kinase / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate kinase

Mass: 21872.799 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: cysC, slr0676 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P72940, adenylyl-sulfate kinase

-
Non-polymers , 6 types, 109 molecules

#2: Chemical	ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₁₀PS
#3: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-CAC / CACODYLATE ION / dimethylarsinate Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆AsO₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.88 Å³/Da / Density % sol: 57.29 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate trihydrate, pH 6.5, 0.2 M magnesium acetate tetrahydrate, 20% PEG 8000, 5 mM adenosine-5'-phosphosulfate, 5 mM beta, gamma-imidoadenosine-5'-triphosphate PH range: 6.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.786→40.4 Å / Num. obs: 37195 / % possible obs: 99.9 % / Redundancy: 3.5 % / R_merge(I) obs: 0.148 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.79→2.84 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.823 / Mean I/σ(I) obs: 2 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4FXP

4fxp

Resolution: 2.79→40.34 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.218	1855	4.99 %
R_work	0.164	-	-
obs	0.167	37155	99.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.79→40.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8130	0	365	88	8583

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8648
X-RAY DIFFRACTION	f_angle_d	1.235	11782
X-RAY DIFFRACTION	f_dihedral_angle_d	22.616	3352
X-RAY DIFFRACTION	f_chiral_restr	0.05	1360
X-RAY DIFFRACTION	f_plane_restr	0.006	1447

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 (%)
2.7863-2.8617	0.3245	137	0.267	2594	X-RAY DIFFRACTION	95
2.8617-2.9458	0.3107	141	0.2347	2711	X-RAY DIFFRACTION	100
2.9458-3.0409	0.3165	150	0.2284	2716	X-RAY DIFFRACTION	100
3.0409-3.1495	0.2892	135	0.2269	2699	X-RAY DIFFRACTION	100
3.1495-3.2756	0.2807	128	0.2132	2739	X-RAY DIFFRACTION	100
3.2756-3.4246	0.2431	129	0.1931	2728	X-RAY DIFFRACTION	100
3.4246-3.605	0.2426	131	0.176	2720	X-RAY DIFFRACTION	100
3.605-3.8307	0.2216	151	0.1607	2727	X-RAY DIFFRACTION	100
3.8307-4.1263	0.1796	156	0.1472	2694	X-RAY DIFFRACTION	100
4.1263-4.541	0.1896	148	0.1215	2724	X-RAY DIFFRACTION	100
4.541-5.1969	0.1702	138	0.1215	2748	X-RAY DIFFRACTION	100
5.1969-6.543	0.2174	168	0.1566	2724	X-RAY DIFFRACTION	100
6.543-40.3465	0.1722	143	0.1432	2776	X-RAY DIFFRACTION	99

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	3.6755	-2.1427	-0.14	5.8632	0.0125	6.1254	-0.149	-0.1815	0.3284	0.5053	0.0174	-0.6574	-0.0247	0.1667	0.0904	0.3399	-0.0416	0.087	0.2755	0.0678	0.463	-14.4894	0.7193	-19.652
2	3.3373	0.7537	0.415	3.8577	-3.5432	7.1977	0.0884	-0.0062	0.1474	0.346	-0.3108	-0.3649	-0.0022	0.9158	0.151	0.3951	0.0376	0.0748	0.3653	0.0448	0.4058	-6.1717	4.0624	-26.6386
3	1.9864	-0.3511	2.0459	2.4242	0.2496	2.4	0.1185	0.0125	-0.4876	0.0689	-0.1549	-0.0998	0.6598	0.2929	0.0352	0.4449	0.0235	0.0521	0.2717	0.0529	0.4483	-10.2485	-5.1362	-30.8018
4	4.1491	4.0944	0.7348	5.5169	-0.2883	8.5477	0.5695	-0.244	0.1483	-0.0755	0.074	0.0442	-0.1779	-0.1864	-0.1754	0.3615	0.0041	0.1149	0.4009	0.0516	0.3984	-28.695	10.5103	-29.9047
5	1.7855	0.9838	-0.3324	4.7401	-1.2568	3.6418	0.1391	0.0531	-0.1706	-0.1169	-0.2987	-0.047	0.0145	0.0065	-0.0397	0.2335	-0.0247	0.0779	0.2964	0.0198	0.4643	-21.6955	8.2132	-36.5996
6	9.4159	-5.5884	-1.7853	3.5627	0.6303	2.7265	-0.0647	0.8149	-0.2528	0.0856	-0.9989	-0.1117	0.033	-0.7758	0.6481	0.5058	0.0098	0.06	0.453	-0.0728	0.3591	-28.5753	0.8129	-21.3891
7	7.0092	-3.2263	-1.2398	2.0648	0.089	4.7357	-0.4896	-0.7629	-0.9205	1.0167	0.4275	0.2305	0.7657	-0.3877	0.1013	0.641	-0.0419	0.0673	0.4718	0.1045	0.4311	-19.3639	-7.5369	-13.9619
8	2.4694	-0.4199	-0.3896	4.9714	1.6986	3.1935	-0.0971	-0.9089	0.5576	0.3158	0.0619	-0.3862	0.0365	0.1231	0.0129	0.3277	-0.0978	0.057	0.5296	-0.1602	0.5097	-34.6484	14.8466	-5.1684
9	4.9274	6.6296	0.8091	8.92	0.8291	0.3926	0.8639	-1.1732	-0.2815	0.4342	-0.5202	-0.8067	-0.0758	0.1348	-0.3066	0.4176	-0.2015	0.0712	0.8192	-0.3003	0.7357	-38.7123	12.9804	1.386
10	2.0036	-0.6963	-2.7732	9.1637	-2.7191	5.5583	-0.3237	-1.3331	-0.1247	0.6003	0.0086	-0.4814	0.0611	0.0479	-0.1007	0.4253	-0.2432	0.0547	0.7573	-0.0157	0.4523	-53.4148	8.1191	-1.0811
11	0.5638	-0.0401	1.1473	2.0519	1.0259	3.9865	0.0446	-0.4571	0.35	-0.087	-0.2947	-0.1069	-0.1527	-0.452	0.1922	0.3188	-0.0492	0.062	0.4949	-0.1054	0.5528	-46.8674	20.7116	-4.2627
12	3.2054	0.7342	0.1095	3.5472	0.3134	1.5632	0.1223	0.2591	0.2882	-0.0954	-0.0311	-0.1109	0.0105	-0.1035	-0.0552	0.4183	-0.0458	0.0908	0.4824	-0.0248	0.3761	-43.5929	8.3616	-18.3489
13	4.0515	-1.156	-0.5567	8.1441	1.6388	4.0355	-0.1941	0.0976	0.749	-0.4439	0.6539	-0.8123	-0.694	0.7727	-0.5747	0.4064	-0.1802	0.1061	0.6013	-0.0917	0.8011	-27.9459	23.2772	-8.1421
14	3.9571	0.5151	1.8005	6.0084	1.1486	5.0599	-0.5206	-0.0929	-0.6174	0.7425	0.3784	-0.5323	0.2848	0.5781	0.2525	0.5392	0.0926	0.1028	0.4625	0.1684	0.4697	-67.8642	-28.3634	16.8404
15	2.6825	-1.0281	-0.2009	2.6122	-2.1237	2.5652	0.0618	-0.1629	-0.3749	-0.2761	-0.38	-0.922	0.2462	0.4261	0.2984	0.4116	0.0819	0.0051	0.4263	0.0333	0.4519	-65.7111	-20.6984	8.7399
16	3.7313	-2.0315	-1.3439	5.1723	3.1339	4.4497	-0.3166	0.0456	-0.6302	-0.0596	-0.0373	0.534	0.0757	-0.1889	0.3055	0.2392	-0.0136	0.0188	0.2733	0.0191	0.3195	-76.1215	-20.8033	7.4297
17	1.1381	0.4504	0.1244	2.4996	0.5909	0.7716	-0.2399	-0.3601	-0.1899	1.1812	0.1771	-0.3416	0.4227	0.271	0.0214	0.8393	0.1157	-0.1042	0.6383	0.0695	0.3743	-70.4221	-12.6001	23.7777
18	2.815	-2.4106	-0.0165	4.0526	1.9324	4.5868	-0.4704	-0.0899	-0.0063	0.9918	0.4243	1.5887	0.2937	-0.266	0.1732	0.5756	-0.0052	0.233	0.4927	-0.0532	0.4433	-81.8089	-18.2107	20.2048
19	2.8123	1.2576	1.4579	4.078	3.6098	5.9177	-0.0626	-0.2331	-0.5073	1.2079	0.2761	-0.2004	0.2018	-0.2276	-0.2968	1.0027	0.1238	0.0831	0.5412	0.2274	0.5752	-73.3929	-33.6545	23.4628
20	2.4696	-0.5008	-2.0002	2.9232	0.8151	5.1294	-0.1448	0.0413	-0.6283	0.004	0.1046	0.198	0.8792	-0.1977	-0.0515	0.5867	0.1357	0.0391	0.4716	0.0544	0.6121	17.145	-9.3916	-26.1311
21	1.762	-0.7107	0.799	7.7349	-7.4678	8.6636	0.3682	-0.0954	-0.6619	0.4075	0.1194	0.7568	0.3541	0.1629	-0.3852	0.5626	0.1282	-0.0511	0.4342	0.0441	0.5622	8.5221	-5.2666	-32.3866
22	3.7998	-0.1524	-1.0282	2.1186	-0.7752	2.8777	-0.0221	-0.3574	-0.2574	0.2488	0.0896	-0.11	0.267	0.4505	0.0418	0.4084	0.1097	-0.0309	0.3742	-0.0035	0.343	12.3635	2.9859	-26.4043
23	3.7297	0.5983	1.0075	1.4233	-0.7205	9.6557	0.0422	-0.0313	-0.4539	0.0999	0.1762	-0.6506	0.5725	0.87	-0.2018	0.3643	0.1324	0.0212	0.589	-0.0122	0.5372	25.4785	-1.4892	-45.0045
24	1.635	-1.4917	-0.5243	5.9025	-1.8133	3.1291	-0.071	-0.6927	-0.2282	0.2023	-0.2693	-0.7037	0.6075	1.3618	0.4568	0.4553	0.2065	-0.061	0.8448	-0.0006	0.6217	27.7366	-0.1641	-28.0667
25	7.1754	-1.372	-0.1324	5.3827	1.3633	3.0146	-0.8855	-2.1983	-1.1877	0.9706	-0.0296	-0.3798	0.9239	1.4054	0.7363	0.9275	0.3556	-0.0225	0.9211	0.2474	0.6611	22.0726	-10.0141	-16.2324
26	3.4382	-1.0674	1.1501	3.1888	0.1755	3.5776	-0.3047	-0.2878	0.5698	0.3515	0.1612	-0.3027	-0.7246	0.1218	0.132	0.4815	-0.0863	-0.0777	0.3562	-0.0647	0.5505	16.6797	43.8172	-45.0539
27	2.6639	1.2995	0.1067	7.6346	0.8899	2.6142	-0.0708	-0.4855	0.6816	0.5253	0.0199	0.5367	-0.4172	0.0861	-0.0089	0.4463	0.0279	-0.0226	0.3472	-0.0807	0.4513	8.2138	36.1397	-45.1612
28	3.7224	-1.8811	0.0386	3.5064	-0.1148	2.794	-0.1042	0.2061	0.445	-0.6532	0.1467	0.0627	-0.4018	0.2213	0.0092	0.4048	-0.0872	-0.0422	0.2432	0.0076	0.3674	9.9926	36.106	-55.5261
29	3.1158	1.6843	-0.8749	3.4772	2.1015	2.7975	0.2001	0.107	-0.3145	-0.0903	0.2748	-0.8765	-0.188	0.6837	-0.3368	0.4859	-0.2428	-0.1348	0.4801	-0.0588	0.8196	25.0743	36.1066	-48.9022
30	8.4044	0.2505	0.0809	8.6334	-2.7265	5.9931	0.4693	-0.2798	0.9144	0.5422	0.1488	-0.7347	0.1082	-0.0534	-0.7194	0.2966	0.0046	-0.0551	0.4916	-0.0927	0.4497	23.0289	20.8254	-42.1839
31	2.8297	-1.0425	0.3992	3.1053	-0.3462	2.333	0.0479	0.0558	0.9577	0.2048	-0.3245	-1.1517	-0.7718	0.5359	0.1905	0.6437	-0.2375	0.0568	0.5049	-0.0413	0.8844	24.2684	45.1613	-50.7924
32	4.2782	-1.7039	-0.0336	1.537	0.5576	1.1734	0.4049	0.9495	0.8541	0.7543	-0.2477	-0.0942	-0.6793	0.1476	0.0109	0.5191	-0.09	-0.0884	0.795	-0.143	0.5156	-50.3878	18.9389	23.3138
33	6.5924	1.3096	-5.3159	4.4073	-3.7564	5.9861	0.1676	0.673	0.6135	0.3611	0.542	-0.4759	-0.5322	0.1333	-0.5594	0.5669	-0.0731	-0.0291	0.6117	-0.0723	0.4921	-50.1429	29.8634	22.732
34	4.8852	4.1126	4.0048	7.7459	5.1091	4.3752	0.2006	-0.0307	0.0892	-0.0271	-0.2582	-0.6517	-1.3377	0.0959	-0.0501	0.6951	-0.1372	-0.1097	0.6306	-0.1396	0.4236	-50.2223	24.7392	14.9545
35	4.3981	1.6793	0.1745	3.1424	0.8711	4.099	0.0022	-0.2517	-0.0475	0.1773	0.1942	-0.3271	-0.115	0.1879	-0.1592	0.3983	0.0052	-0.0771	0.4919	-0.1161	0.3869	-52.1235	13.1409	18.3913
36	1.4187	-1.0957	-0.8076	2.2507	3.3047	9.3414	0.1325	-0.3081	0.4474	0.81	0.3792	0.2426	-0.4105	0.7112	-0.3931	0.3855	-0	0.0058	0.6234	-0.1063	0.411	-71.8898	16.4174	23.2863
37	3.3543	1.2407	0.4851	3.3833	0.453	0.3218	0.5795	-1.1652	0.3767	1.0755	-0.3056	-0.4948	-0.1846	0.5234	-0.2306	0.873	-0.1362	-0.2	1.0742	-0.2613	0.6509	-48.8171	20.6043	31.5993

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 31 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 32 THROUGH 55 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 56 THROUGH 108 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 109 THROUGH 117 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 118 THROUGH 148 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 149 THROUGH 157 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 158 THROUGH 176 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 4 THROUGH 31 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 32 THROUGH 46 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 47 THROUGH 55 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 56 THROUGH 107 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 108 THROUGH 157 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 158 THROUGH 176 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 4 THROUGH 31 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 32 THROUGH 55 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 56 THROUGH 99 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 100 THROUGH 138 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 139 THROUGH 148 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 149 THROUGH 176 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 4 THROUGH 31 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 32 THROUGH 55 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 56 THROUGH 108 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 109 THROUGH 138 )
24	X-RAY DIFFRACTION	24	CHAIN 'D' AND (RESID 139 THROUGH 157 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 158 THROUGH 176 )
26	X-RAY DIFFRACTION	26	CHAIN 'E' AND (RESID 4 THROUGH 31 )
27	X-RAY DIFFRACTION	27	CHAIN 'E' AND (RESID 32 THROUGH 55 )
28	X-RAY DIFFRACTION	28	CHAIN 'E' AND (RESID 56 THROUGH 99 )
29	X-RAY DIFFRACTION	29	CHAIN 'E' AND (RESID 100 THROUGH 117 )
30	X-RAY DIFFRACTION	30	CHAIN 'E' AND (RESID 118 THROUGH 138 )
31	X-RAY DIFFRACTION	31	CHAIN 'E' AND (RESID 139 THROUGH 176 )
32	X-RAY DIFFRACTION	32	CHAIN 'F' AND (RESID 4 THROUGH 17 )
33	X-RAY DIFFRACTION	33	CHAIN 'F' AND (RESID 18 THROUGH 31 )
34	X-RAY DIFFRACTION	34	CHAIN 'F' AND (RESID 32 THROUGH 46 )
35	X-RAY DIFFRACTION	35	CHAIN 'F' AND (RESID 47 THROUGH 115 )
36	X-RAY DIFFRACTION	36	CHAIN 'F' AND (RESID 116 THROUGH 138 )
37	X-RAY DIFFRACTION	37	CHAIN 'F' AND (RESID 139 THROUGH 176 )

-
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, 6 molecules ABCDEF

-
Non-polymers , 6 types, 109 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 , 6 types, 109 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 , 6 types, 109 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