PDB-3zzi: Crystal structure of a tetrameric acetylglutamate kinase from Sac...

ID or keywords:

Entry

Database: PDB / ID: 3zzi

Title

Crystal structure of a tetrameric acetylglutamate kinase from Saccharomyces cerevisiae

Components

ACETYLGLUTAMATE KINASE

Keywords

TRANSFERASE / ARGININE BIOSYNTHESIS

Function / homology

Function and homology information

Urea cycle / ornithine biosynthetic process / N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process / NADP+ binding / NAD binding / mitochondrial matrix ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.8 Å

Authors

de Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V.

Citation

Journal: Plos One / Year: 2012
Title: Insight on an Arginine Synthesis Metabolon from the Tetrameric Structure of Yeast Acetylglutamate Kinase
Authors: De Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V.

History

Deposition	Sep 1, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 2, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2012	Group: Other
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	May 15, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim 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_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

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3zzi.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb3zzi.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	3zzi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3zzfSC 3zzgC 3zzhC 4ab7C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4ab7-1 4ab7-2 3s6k-1 6aqh-d 3e8k-d 5zal-d 3jv2-d 4x6c-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: ACETYLGLUTAMATE KINASE

E: ACETYLGLUTAMATE KINASE

F: ACETYLGLUTAMATE KINASE

G: ACETYLGLUTAMATE KINASE

H: ACETYLGLUTAMATE KINASE

411 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: ACETYLGLUTAMATE KINASE

defined by author&software
205 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: ACETYLGLUTAMATE KINASE

F: ACETYLGLUTAMATE KINASE

G: ACETYLGLUTAMATE KINASE

H: ACETYLGLUTAMATE KINASE

defined by author&software
205 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	95.240, 111.290, 113.140
Angle α, β, γ (deg.)	75.77, 89.29, 69.12
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 67 - 502 / Label seq-ID: 18 - 453

NCS ensembles :

#1: Protein	ACETYLGLUTAMATE KINASE / N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ...N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ARG5\ / 6\ / MITOCHONDRIAL Mass: 51340.094 Da / Num. of mol.: 8 / Fragment: N-ACETYLGLUTAMATE KINASE DOMAIN, RESIDUES 58-513 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: SIGMA 1278B / Plasmid: PYK6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01217, acetylglutamate kinase

#1: Protein

ACETYLGLUTAMATE KINASE / N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ...

Mass: 51340.094 Da / Num. of mol.: 8 / Fragment: N-ACETYLGLUTAMATE KINASE DOMAIN, RESIDUES 58-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: SIGMA 1278B / Plasmid: PYK6 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01217, acetylglutamate kinase

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION OF SURFACE EXPOSED LYSINES WITH ABC PREVIOUS TO CRYSTALLIZATION. 10 MG/ML PROTEIN IN 20MM HEPES PH 7.5, 0.5 M NACL, 1MM MSH, AND SUPPLEMENTED ...Details: PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION OF SURFACE EXPOSED LYSINES WITH ABC PREVIOUS TO CRYSTALLIZATION. 10 MG/ML PROTEIN IN 20MM HEPES PH 7.5, 0.5 M NACL, 1MM MSH, AND SUPPLEMENTED WITH 40 MM NAG, WAS CRYSTALLIZED IN PRESENCE OF 0.2 M AMMONIUM CITRATE PH 7.0 AND 12 % PEG3350 AS CRYSTALLIZATION SOLUTION, IN SITTING DROPS AT 4C. CRYOBUFFER SOLUTION WAS THAT OF CRYSTALLIZATION WITH PEG3350 ENRICHED TO 40 %.

Crystal

Density Matthews: 2.64 Å³/Da / Density % sol: 54 % / Description: NONE

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION OF SURFACE EXPOSED LYSINES WITH ABC PREVIOUS TO CRYSTALLIZATION. 10 MG/ML PROTEIN IN 20MM HEPES PH 7.5, 0.5 M NACL, 1MM MSH, AND SUPPLEMENTED ...

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
Detector	Type: ADSC CCD / Detector: CCD / Date: Mar 3, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9393 Å / Relative weight: 1
Reflection	Resolution: 3.8→109 Å / Num. obs: 39773 / % possible obs: 96.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2.4 % / R_merge(I) obs: 0.057 / Net I/σ(I): 10.5
Reflection shell	Resolution: 3.8→4.01 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.455 / Mean I/σ(I) obs: 1.5 / % possible all: 96.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZZF FOR ONE DOMAIN, AND AN INCOMPLETE TRACING FROM OTHER CRYSTAL OF THE SAME PRESENT PROTEIN FOR THE SECOND DOMAIN

3zzf

Resolution: 3.8→109.11 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.905 / SU B: 97.46 / SU ML: 0.608 / Cross valid method: THROUGHOUT / ESU R Free: 0.791 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23592	1985	5 %	RANDOM
R_work	0.19725	-	-	-
obs	0.19914	37381	95.33 %	-

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: 127.643 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.52 Å²	1.34 Å²	-1.42 Å²
2-	-	-0.06 Å²	0.68 Å²
3-	-	-	-0.67 Å²

Refinement step

Cycle: LAST / Resolution: 3.8→109.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27248	0	0	0	27248

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	27712
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	18610
X-RAY DIFFRACTION	r_angle_refined_deg	1.793	1.966	37526
X-RAY DIFFRACTION	r_angle_other_deg	1.831	3	45630
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.1	5	3480
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.199	24.926	1222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.196	15	4958
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.305	15	142
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	4336
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	30710
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	5416
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	15833	0.06
1	2	B	15833	0.06
2	1	A	15812	0.06
2	2	C	15812	0.06
3	1	A	15220	0.1
3	2	D	15220	0.1
4	1	A	16013	0.03
4	2	E	16013	0.03
5	1	A	15637	0.07
5	2	F	15637	0.07
6	1	A	15913	0.04
6	2	G	15913	0.04
7	1	A	15088	0.11
7	2	H	15088	0.11
8	1	B	15906	0.04
8	2	C	15906	0.04
9	1	B	15249	0.1
9	2	D	15249	0.1
10	1	B	15845	0.06
10	2	E	15845	0.06
11	1	B	15705	0.07
11	2	F	15705	0.07
12	1	B	15872	0.05
12	2	G	15872	0.05
13	1	B	15167	0.11
13	2	H	15167	0.11
14	1	C	15299	0.1
14	2	D	15299	0.1
15	1	C	15879	0.06
15	2	E	15879	0.06
16	1	C	15738	0.07
16	2	F	15738	0.07
17	1	C	15920	0.06
17	2	G	15920	0.06
18	1	C	15218	0.11
18	2	H	15218	0.11
19	1	D	15275	0.11
19	2	E	15275	0.11
20	1	D	15110	0.12
20	2	F	15110	0.12
21	1	D	15300	0.1
21	2	G	15300	0.1
22	1	D	15576	0.08
22	2	H	15576	0.08
23	1	E	15701	0.07
23	2	F	15701	0.07
24	1	E	15956	0.05
24	2	G	15956	0.05
25	1	E	15146	0.11
25	2	H	15146	0.11
26	1	F	15694	0.07
26	2	G	15694	0.07
27	1	F	15349	0.1
27	2	H	15349	0.1
28	1	G	15174	0.11
28	2	H	15174	0.11

LS refinement shell

Resolution: 3.8→3.899 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	135	-
R_work	0.29	2385	-
obs	-	-	83.11 %

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	19.5404	5.6881	-10.2533	41.5135	-6.7009	31.0856	-2.095	1.0212	-3.3283	1.1139	-0.5201	0.6669	2.2618	0.3404	2.615	0.4938	-0.1637	0.1954	0.9661	-0.123	1.3307	-10.301	-3.593	-24.53
2	17.7553	-5.2168	6.447	36.5325	-2.7129	25.181	-0.7679	-1.4207	-0.7484	1.7482	1.5412	-1.6757	1.3589	0.5254	-0.7733	0.6808	-0.0848	-0.0458	0.6811	0.0646	0.7853	11.6	23.37	9.523
3	41.0021	1.8821	-4.9564	20.8858	-2.7476	15.7639	-0.1494	-0.8485	3.0929	-0.8537	0.1277	-1.5087	-1.7037	1.1162	0.0217	1.1938	-0.3972	-0.4507	0.732	-0.075	0.9815	49.691	46.945	-28.914
4	8.4774	2.2478	1.8218	13.4992	-5.4916	4.6762	-1.2471	-0.7274	0.0732	0.8712	1.7262	-0.2541	0.7274	-1.379	-0.4791	2.0685	-0.1172	-0.1017	1.7458	-0.2987	1.2479	44.98	13.762	5.627
5	4.2488	9.9136	1.3521	27.2747	2.2844	16.4145	-0.6949	0.8581	0.0292	-1.1981	-0.3261	-0.3775	-0.9251	0.0381	1.0211	0.914	-0.0927	-0.1428	1.5871	0.2003	1.1767	-7.493	3.93	-32.499
6	17.7177	-5.0664	9.7947	29.4107	-3.653	25.5602	-1.7617	0.3222	1.9814	-0.1191	1.0409	0.76	-1.2558	-1.1801	0.7208	0.6283	-0.3581	0.121	0.7604	0.2493	1.0284	6.996	32.583	4.37
7	10.4147	12.3515	-7.6592	24.9861	0.9268	33.8632	-1.1861	1.0064	-1.3451	-1.1141	-0.0458	0.1694	2.8658	-1.1642	1.2319	1.0235	-0.4481	0.3172	1.1052	-0.6973	1.9143	43.243	6.893	-3.227
8	11.2944	-11.2856	-0.3994	46.0627	-20.0731	12.3148	0.4727	3.0011	1.636	4.5784	-0.6678	-1.0315	-3.2844	-1.2888	0.1951	1.5087	-0.178	-0.3784	1.5275	0.6111	1.6054	38.796	43.937	-32.362
9	8.4176	1.2695	2.7099	8.113	-3.4246	8.0908	0.629	0.0958	-1.2815	0.479	-0.2337	-0.8688	1.4329	1.0102	-0.3952	0.5881	0.1211	-0.1104	0.719	-0.1355	0.926	0.526	-16.913	-1.735
10	7.106	0.9733	1.8604	11.4719	-1.3116	7.1395	0.4279	-0.7384	-0.741	1.6195	0.1673	0.2428	0.7167	-0.2777	-0.5952	0.6119	-0.1254	-0.0653	0.7876	0.0699	0.6759	1.643	-3.198	15.679
11	6.0311	2.3954	1.6628	11.735	0.0997	10.9988	-0.289	-0.8142	0.8366	0.6838	0.236	-0.4826	-1.2953	0.5005	0.0531	0.8163	-0.2347	0.1129	0.8754	-0.2096	0.8423	63.601	51.057	-4.422
12	10.0319	1.9569	1.2482	10.5957	-0.2475	7.8556	-0.4866	-0.5591	0.0527	1.1178	0.4062	-1.3105	-0.5001	1.0361	0.0804	0.6358	-0.105	0.11	1.0902	-0.0556	0.6344	66.734	31.851	6.277
13	5.0939	1.9185	1.4913	14.7689	-3.2059	7.9038	0.0849	0.304	0.4766	0.174	0.392	1.0052	-0.1796	-1.4078	-0.4769	0.6543	0.0174	0.1002	0.9928	0.003	0.5672	-8.484	32.629	-35.152
14	4.3246	1.8269	-0.4592	8.93	-2.5241	9.3175	0.4595	-0.0991	0.5161	0.6457	-0.4808	-0.3974	-0.3879	-0.4407	0.0213	0.9547	-0.0284	0.0556	0.5113	0.0291	0.6788	6.214	43.272	-22.464
15	8.3026	0.1499	3.6839	10.4778	2.5561	10.0693	0.1161	-0.0284	-0.5352	-0.3344	-0.57	1.7298	0.1853	-1.0469	0.4539	0.1111	-0.0535	0.1816	0.3994	-0.1725	0.9612	27.41	3.021	-26.492
16	5.6465	-0.8109	2.9201	13.8005	1.7702	7.736	0.3485	0.8914	-0.3523	-1.7017	-0.3059	0.3335	0.2408	0.3805	-0.0426	0.5291	0.0934	0.0449	0.5698	-0.1539	0.5414	31.96	17.94	-42.13
17	12.9431	3.4287	2.9297	15.1087	4.6508	10.7266	-0.0254	1.8276	-1.7247	-1.7601	0.5255	-0.8171	1.8676	1.3303	-0.5002	1.0312	0.2459	-0.2661	1.0352	-0.4052	0.9526	-11.119	-24.877	-19.49
18	18.1454	-0.8812	4.4953	6.9662	-0.1861	18.7683	0.2195	-1.47	0.2333	1.7078	-0.0275	-0.2722	-0.554	-0.2811	-0.192	1.0916	-0.3302	-0.1538	0.6339	0.0688	0.7838	12.038	11.735	28.675
19	14.0724	-2.4621	-0.2368	28.7586	-5.3762	11.6689	-0.5463	1.0058	2.2129	-1.4463	0.2097	-0.6854	-0.8351	-0.3365	0.3366	1.4753	-0.4016	0.0149	0.8776	0.0553	1.0827	63.473	63.217	-23.041
20	5.8449	-8.374	2.409	19.4178	3.4537	22.4086	1.0001	-0.8816	-0.3318	-0.0548	-0.5404	-1.8677	0.8276	-0.6774	-0.4597	1.1689	-0.425	-0.145	1.4152	0.4665	1.5061	62.597	17.598	20.48
21	15.8631	3.6125	2.0022	6.3918	-1.2517	22.2754	0.2221	0.9046	-0.2707	0.1322	0.0021	0.6956	0.6098	-1.461	-0.2242	0.8196	-0.1932	-0.0094	1.1766	-0.0385	0.8342	-14.564	19.059	-49.099
22	31.4391	-9.4059	3.9001	19.3987	3.91	15.8879	-1.7844	-0.8225	6.1857	1.9533	0.5153	-3.9077	-1.7974	-0.2843	1.2691	1.9618	-0.1829	-0.7597	0.8288	-0.1288	2.1002	11.889	53.244	-3.654
23	22.6228	-3.049	-0.0553	24.9562	-9.523	10.0226	0.2088	-1.5681	-1.0319	2.7622	0.4699	1.8901	0.0465	-1.1459	-0.6787	0.6869	-0.3596	0.3124	0.6498	0.1851	0.8063	33.362	-11.405	-10.297
24	9.8554	-3.6528	1.7047	11.4368	-3.1231	16.698	0.256	1.3708	0.6227	-1.6197	-0.6294	-0.5491	-1.7909	0.1982	0.3734	1.3212	0.1152	0.0067	0.5887	-0.0783	0.8441	28.189	37.605	-52.074
25	20.5981	-8.571	-0.364	26.9778	1.1261	15.2243	-0.171	-0.4074	0.5479	1.6402	0.4438	-0.784	0.1397	-1.0396	-0.2728	0.1984	-0.096	0.1587	0.5908	-0.0743	0.5596	-40.674	-15.249	-26.753
26	24.0081	8.6291	2.5088	25.7958	4.6488	23.5394	0.4298	2.4741	-0.5394	-1.3101	1.1044	-2.3158	0.1864	2.3145	-1.5341	0.6881	0.1145	0.1695	1.2667	-0.428	0.9606	39.935	26.802	27.716
27	9.3048	-2.4665	2.6514	26.8299	-4.0531	20.2526	0.4645	1.6209	-0.7619	-0.8037	0.117	-0.2194	1.8161	1.6502	-0.5816	1.3142	-0.1068	0.3925	1.7574	0.8679	1.7029	70.724	57.07	-54.098
28	30.3263	6.1803	4.0072	26.6809	-8.9574	25.0206	0.0262	-1.9666	0.5481	0.86	0.646	3.2969	0.9231	-2.7731	-0.6722	0.8119	-0.1297	0.3668	1.4804	-0.1726	1.0734	43.691	4.457	41.82
29	21.6846	-3.6914	-5.9865	36.3535	12.0754	20.3146	-0.6372	0.8638	-1.4751	-0.6832	1.8399	-4.0204	-0.1157	2.2809	-1.2027	1.3314	-0.4291	0.1236	1.703	-0.1429	1.0632	-8.46	-2.356	-70.354
30	21.2834	4.9966	1.885	4.5673	1.2626	20.6119	-0.5366	-1.738	0.2063	0.9525	0.651	1.0008	-0.5588	-2.4103	-0.1144	2.4579	1.0084	-0.2294	1.7834	-0.4084	2.1312	-2.983	60.842	23.389
31	31.1531	6.2142	-2.3335	7.7408	-0.0203	14.8437	-0.5916	1.0194	1.5225	-0.3251	0.3028	0.1969	-0.003	0.7329	0.2887	0.7584	-0.0509	-0.0745	0.4319	-0.0364	0.8407	63.184	-19.639	-3.37
32	13.0553	-6.782	-5.8702	51.5601	0.7987	23.6041	0.8099	-0.9584	0.8996	1.7206	-1.0961	0.7144	-0.8709	0.5237	0.2862	1.0787	0.206	0.1715	0.9231	0.2682	0.8497	16.645	65.675	-47.962
33	12.8838	-3.2984	3.9272	9.8014	5.9335	25.4305	0.6529	1.4287	-0.3591	0.1161	0.2923	-0.7703	1.1531	0.7955	-0.9452	0.2326	-0.0666	0.1203	0.4434	-0.0756	0.6833	-32.95	-17.578	-35.714
34	16.1517	-0.5865	5.705	17.0177	9.4397	22.9378	0.2518	-0.0162	0.1651	0.9454	0.2885	0.1506	0.7585	0.3428	-0.5403	0.4641	0.0497	0.0702	0.4635	-0.129	0.5254	29.169	30.905	31.179
35	18.1149	-2.2441	9.4306	13.9239	-4.3022	23.1757	0.034	0.6402	1.5373	2.1834	-0.2531	-0.1977	-0.1831	-0.7976	0.2191	1.3132	-0.3872	0.598	1.1182	0.6396	1.2131	61.536	63.303	-49.365
36	21.1631	-11.6482	2.3584	16.2838	-1.9872	14.8617	0.6352	-0.4646	0.8924	0.1334	-0.6344	0.2588	1.1363	0.875	-0.0008	0.5971	-0.0966	0.2277	0.8235	-0.1819	0.5688	52.442	2.533	33.749
37	37.0543	7.0419	2.6661	25.0445	9.2753	6.9291	-0.1173	-0.9223	1.8194	-0.0712	0.3609	-0.13	-0.5457	0.011	-0.2436	1.3597	-0.1964	0.2366	1.1574	0.1172	0.3139	-16.85	0.835	-62.185
38	14.1235	6.7249	7.1763	14.5513	6.4724	21.4226	-1.1413	0.2772	0.5774	-0.0847	0.0856	1.422	-2.963	-1.4926	1.0557	1.839	0.8115	-0.3949	0.9591	-0.306	1.3781	8.323	57.542	20.771
39	13.8697	-1.868	4.4962	17.9781	-6.7459	13.7754	-0.4693	-0.9107	0.3001	0.9249	1.0606	0.2946	0.7974	-0.9809	-0.5912	1.0186	-0.0902	0.051	0.3375	-0.2063	0.6544	55.266	-18.629	5.671
40	16.5554	0.2226	-6.6468	19.4615	-9.7604	20.6342	0.1133	0.4489	-0.2637	-1.2539	-0.4945	0.3356	0.4045	-0.1591	0.3813	1.2537	0.1776	0.157	0.5268	0.1517	0.8662	26.274	60.517	-53.135
41	10.9496	0.6563	5.2707	18.8121	-1.8746	18.8975	-0.2356	1.5641	1.0248	-1.3025	-0.0557	1.0713	-0.4185	-0.41	0.2913	0.317	0.0166	0.1999	0.7932	-0.0639	0.645	-34.39	-10.651	-47.48
42	5.4128	1.8233	6.6339	29.0414	5.3121	20.5447	-1.1907	-0.2537	1.2638	-0.2368	0.5583	-0.7376	-1.9804	1.0428	0.6324	0.5977	0.0537	0.0785	0.728	-0.2351	0.7653	26.996	44.459	30.852
43	11.6284	2.0249	7.9582	17.8809	-8.7857	17.8492	0.1098	1.0818	0.0735	0.15	-0.5786	0.1016	-0.7899	0.7257	0.4688	1.0809	0.021	0.562	1.079	0.2717	0.9265	50.316	65.105	-57.053
44	13.2574	1.3648	-0.9821	23.9941	3.3689	14.4629	-0.0905	-0.7557	-1.2323	0.1814	-0.3626	0.0143	2.2141	0.18	0.4531	0.7635	0.0099	0.2962	0.8801	0.0984	0.5691	54.255	-10.256	29.123
45	18.9134	4.2443	4.3968	19.5627	-0.6818	12.7471	-0.3966	0.1075	-0.3996	-1.342	-0.0843	0.6802	0.3582	-0.8461	0.4809	0.6991	0.0171	0.3268	1.0623	-0.0837	0.476	-25.849	-8.725	-58.191
46	10.5952	1.9333	10.5473	16.5547	1.5612	27.5882	-0.5676	-0.7086	0.5965	0.7638	0.1403	0.0455	-2.3862	-0.9439	0.4273	1.0013	0.502	0.0718	0.6342	-0.4147	0.7911	15.93	52.092	30.813
47	12.3966	0.7375	4.2272	11.9707	3.0401	19.9929	-0.4264	-1.4815	-0.8658	0.7776	0.3387	-0.658	0.9092	0.7419	0.0877	0.8291	0.0175	0.2696	0.6111	0.0291	0.6401	60.068	-15.355	18.109
48	16.6903	2.3399	0.865	17.0228	-1.3693	5.6261	0.197	0.3114	1.6162	-0.5438	-0.012	-0.1344	-0.9541	0.3819	-0.185	1.2094	0.2443	0.5664	0.6189	0.2437	0.8992	37.551	68.157	-54.801

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	67 - 97
2	X-RAY DIFFRACTION	2	B	67 - 97
3	X-RAY DIFFRACTION	3	G	67 - 97
4	X-RAY DIFFRACTION	4	H	67 - 97
5	X-RAY DIFFRACTION	5	D	67 - 97
6	X-RAY DIFFRACTION	6	C	67 - 97
7	X-RAY DIFFRACTION	7	E	67 - 97
8	X-RAY DIFFRACTION	8	F	67 - 97
9	X-RAY DIFFRACTION	9	A	98 - 262
10	X-RAY DIFFRACTION	10	B	98 - 262
11	X-RAY DIFFRACTION	11	G	98 - 262
12	X-RAY DIFFRACTION	12	H	98 - 262
13	X-RAY DIFFRACTION	13	D	98 - 262
14	X-RAY DIFFRACTION	14	C	98 - 262
15	X-RAY DIFFRACTION	15	E	98 - 262
16	X-RAY DIFFRACTION	16	F	98 - 262
17	X-RAY DIFFRACTION	17	A	263 - 351
18	X-RAY DIFFRACTION	18	B	263 - 351
19	X-RAY DIFFRACTION	19	G	263 - 351
20	X-RAY DIFFRACTION	20	H	263 - 351
21	X-RAY DIFFRACTION	21	D	263 - 351
22	X-RAY DIFFRACTION	22	C	263 - 351
23	X-RAY DIFFRACTION	23	E	263 - 351
24	X-RAY DIFFRACTION	24	F	263 - 351
25	X-RAY DIFFRACTION	25	A	352 - 407
26	X-RAY DIFFRACTION	26	B	352 - 407
27	X-RAY DIFFRACTION	27	G	352 - 407
28	X-RAY DIFFRACTION	28	H	352 - 407
29	X-RAY DIFFRACTION	29	D	352 - 407
30	X-RAY DIFFRACTION	30	C	352 - 407
31	X-RAY DIFFRACTION	31	E	352 - 407
32	X-RAY DIFFRACTION	32	F	352 - 407
33	X-RAY DIFFRACTION	33	A	408 - 447
34	X-RAY DIFFRACTION	34	B	408 - 447
35	X-RAY DIFFRACTION	35	G	408 - 447
36	X-RAY DIFFRACTION	36	H	408 - 447
37	X-RAY DIFFRACTION	37	D	408 - 447
38	X-RAY DIFFRACTION	38	C	408 - 447
39	X-RAY DIFFRACTION	39	E	408 - 447
40	X-RAY DIFFRACTION	40	F	408 - 447
41	X-RAY DIFFRACTION	41	A	448 - 507
42	X-RAY DIFFRACTION	42	B	448 - 507
43	X-RAY DIFFRACTION	43	G	448 - 507
44	X-RAY DIFFRACTION	44	H	448 - 507
45	X-RAY DIFFRACTION	45	D	448 - 507
46	X-RAY DIFFRACTION	46	C	448 - 507
47	X-RAY DIFFRACTION	47	E	448 - 507
48	X-RAY DIFFRACTION	48	F	448 - 507

-
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