PDB-4fyy: E. coli Aspartate Transcarbamoylase Complexed with CTP, UTP, and Mg2+

ID or keywords:

Entry

Database: PDB / ID: 4fyy

Title

E. coli Aspartate Transcarbamoylase Complexed with CTP, UTP, and Mg2+

Components

(Aspartate carbamoyltransferase ...

) x 2

Keywords

TRANSFERASE / pyrimidine nucleotide biosynthesis /

feedback inhibition /

allostery

Function / homology

Function and homology information

aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process /

aspartate carbamoyltransferase /

aspartate carbamoyltransferase activity /

amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9395 Å

Authors

Cockrell, G.M. / Kantrowitz, E.R.

Citation

Journal: Biochemistry / Year: 2012
Title: Metal Ion Involvement in the Allosteric Mechanism of Escherichia coli Aspartate Transcarbamoylase.
Authors: Cockrell, G.M. / Kantrowitz, E.R.

History

Deposition	Jul 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 10, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 13, 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_site 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4fyy.cif.gz	208.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4fyy.ent.gz	166.2 KB	Display	PDB format
PDBx/mmJSON format	4fyy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/4fyy ftp://data.pdbj.org/pub/pdb/validation_reports/fy/4fyy	HTTPS FTP

-
Related structure data

Related structure data	4fyvC 4fywC 4fyxC 1za1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4fyx-1 1za2-1 2fzg-1 1sku-1 2fzc-1 2qg9-1 1tu0-1 1tug-1 4fyv-1 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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (19)

Deposited unit

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

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

1

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

defined by author&software
315 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.133, 121.133, 141.438
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-432- HOH
2	1	A-543- HOH
3	1	C-582- HOH

-
Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD

#1: Protein	Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase Mass: 34337.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein	Aspartate carbamoyltransferase regulatory chain Mass: 17143.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7F3

-
Non-polymers , 5 types, 582 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₅N₂O₁₅P₃ / Comment: UTP*YM
#5: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.91 Å³/Da / Density % sol: 57.72 %
Crystal grow	Temperature: 298 K / Method: microdialysis / pH: 5.7 Details: 40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM CTP, pH 5.7 (crystals soaked in 5 mM UTP and 5 mM Mg2+), MICRODIALYSIS, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2012

Radiation

Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Redundancy: 22 % / Av σ(I) over netI: 23.19 / Number: 1956459 / R_merge(I) obs: 0.137 / Χ²: 1.16 / D res high: 1.94 Å / D res low: 50 Å / Num. obs: 89121 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.18	50	100	1	0.119	0.732	31.2
3.32	4.18	100	1	0.127	0.999	23
2.9	3.32	100	1	0.138	1.204	21.4
2.63	2.9	100	1	0.166	1.367	21.2
2.44	2.63	100	1	0.196	1.464	21.1
2.3	2.44	100	1	0.236	1.412	20.8
2.18	2.3	100	1	0.28	1.385	20.5
2.09	2.18	100	1	0.344	1.246	20.3
2.01	2.09	100	1	0.461	1.107	20.1
1.94	2.01	100	1	0.608	0.99	19.5

Reflection

Resolution: 1.9395→50 Å / Num. all: 89121 / Num. obs: 89121 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 22 % / R_merge(I) obs: 0.137 / Χ²: 1.165 / Net I/σ(I): 11.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.9395-2.01	19.5	0.608	8794	0.99	1	100
2.01-2.09	20.1	0.461	8832	1.107	1	100
2.09-2.18	20.3	0.344	8830	1.246	1	100
2.18-2.3	20.5	0.28	8841	1.385	1	100
2.3-2.44	20.8	0.236	8870	1.412	1	100
2.44-2.63	21.1	0.196	8853	1.464	1	100
2.63-2.9	21.2	0.166	8891	1.367	1	100
2.9-3.32	21.4	0.138	8923	1.204	1	100
3.32-4.18	23	0.127	9012	0.999	1	100
4.18-50	31.2	0.119	9275	0.732	1	100

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZA1

1za1

Resolution: 1.9395→49.179 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 0 / Phase error: 20.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2365	4462	5.01 %	Random
R_work	0.1926	-	-	-
obs	0.1948	89119	99.98 %	-
all	-	89196	-	-

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 218.39 Å² / B_iso mean: 41.2092 Å² / B_iso min: 12.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.9395→49.179 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7140	0	120	574	7834

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7406
X-RAY DIFFRACTION	f_angle_d	1.139	10083
X-RAY DIFFRACTION	f_chiral_restr	0.077	1165
X-RAY DIFFRACTION	f_plane_restr	0.005	1288
X-RAY DIFFRACTION	f_dihedral_angle_d	15.002	2762

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.9395-1.9615	0.2355	153	0.2003	2784	2937
1.9615-1.9846	0.2702	138	0.1996	2777	2915
1.9846-2.0088	0.2672	155	0.2065	2779	2934
2.0088-2.0342	0.2624	150	0.2111	2772	2922
2.0342-2.061	0.2829	161	0.2017	2829	2990
2.061-2.0892	0.2723	154	0.1924	2770	2924
2.0892-2.1191	0.2151	144	0.1837	2812	2956
2.1191-2.1507	0.2447	140	0.1839	2799	2939
2.1507-2.1843	0.2439	150	0.1839	2780	2930
2.1843-2.2201	0.2341	161	0.175	2768	2929
2.2201-2.2584	0.2533	161	0.1791	2805	2966
2.2584-2.2995	0.2389	124	0.178	2826	2950
2.2995-2.3437	0.2168	151	0.1835	2787	2938
2.3437-2.3915	0.2517	153	0.1837	2800	2953
2.3915-2.4435	0.238	145	0.1812	2828	2973
2.4435-2.5004	0.2089	132	0.1756	2815	2947
2.5004-2.5629	0.2379	157	0.183	2804	2961
2.5629-2.6322	0.2716	136	0.188	2819	2955
2.6322-2.7096	0.2339	148	0.1837	2809	2957
2.7096-2.7971	0.2219	154	0.1898	2807	2961
2.7971-2.897	0.2304	146	0.1909	2827	2973
2.897-3.013	0.2455	146	0.196	2840	2986
3.013-3.1501	0.2683	116	0.2006	2853	2969
3.1501-3.3162	0.2469	151	0.2043	2819	2970
3.3162-3.5239	0.2366	144	0.2014	2842	2986
3.5239-3.7959	0.2399	157	0.1902	2865	3022
3.7959-4.1777	0.2401	145	0.1842	2857	3002
4.1777-4.7818	0.2392	171	0.1811	2858	3029
4.7818-6.0228	0.2116	169	0.1984	2888	3057
6.0228-49.195	0.2129	150	0.2134	3038	3188

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	0.4409	0.0261	0.1733	0.4089	0.2296	0.6311	0.0357	0.0977	-0.026	-0.084	0.0754	0.0678	0.0211	-0.176	0	0.188	0.0149	0.0002	0.2421	0.0248	0.1772	43.2502	36.5727	2.6817
2	0.0978	-0.0949	-0.3011	0.3541	0.3664	0.8996	0.2566	-0.1727	0.0085	-0.1086	0.1729	-0.7141	-0.2553	0.0684	0.2358	0.1626	-0.0196	-0.1175	0.372	0.0633	0.1891	55.0767	43.3671	19.5562
3	0.4153	-0.1225	-0.3213	0.4944	-0.2934	0.6317	0.0048	0.0798	0.076	-0.012	0.1032	0.0555	-0.0096	-0.1423	0	0.1842	0.0186	-0.0001	0.2815	0.0312	0.1588	35.756	36.5006	12.3359
4	0.58	0.1227	-0.2733	0.9564	-0.4522	0.3597	-0.2169	-0.2612	-0.2678	0.3429	0.251	0.1429	0.0986	-0.3637	-0.0036	0.286	0.0414	0.0005	0.3573	0.0581	0.2681	27.1561	22.0259	22.078
5	0.8583	-0.2017	0.0252	0.7808	0.7161	0.5164	0.0285	0.1865	-0.0892	-0.124	-0.0701	-0.0196	0.1336	-0.0441	-0.0001	0.1786	-0.0073	-0.0196	0.2319	-0.0017	0.1658	40.2175	24.6173	7.2453
6	0.3212	0.1691	0.3066	0.123	0.138	0.239	0.4102	0.1774	0.002	-0.4667	-0.4374	0.0839	-0.2379	-0.6111	-0.0579	-0.2467	0.7553	-0.1927	0.2661	0.0014	0.3949	18.6128	79.9689	29.1623
7	0.009	0.0749	0.0314	0.075	0.0727	0.1023	-0.1788	0.3007	-0.0159	-0.1147	0.0381	-0.2356	-0.3114	-0.2493	-0.0016	0.3785	0.0727	-0.0345	0.3509	-0.0557	0.3741	30.4061	74.984	28.0898
8	0.2596	0.025	0.2946	-0.0491	0.0192	0.3648	-0.2343	-0.2077	0.0013	-0.6259	-0.2432	-0.048	0.3531	-0.4546	-0.0184	0.4608	0.1476	0.001	0.3874	-0.0349	0.327	19.3341	77.6574	30.4765
9	0.605	-0.1245	0.4919	0.0218	-0.097	0.4064	0.0771	-0.2645	-0.1261	-0.019	0.3301	-0.2179	-0.0909	0.0942	0.2458	0.6006	0.1569	-0.0206	0.5376	-0.2992	0.6664	22.1413	67.2461	18.8459
10	0.0257	-0.0309	-0.107	0.2476	0.1371	0.1648	-0.0492	0.2079	-0.3719	0.2638	-0.2404	0.2267	-0.2484	-0.4375	-0.0861	0.3378	0.1761	-0.0484	0.3934	-0.1334	0.4749	17.3744	72.1331	23.7328
11	0.9349	0.2437	-0.641	0.0675	-0.1629	0.3775	-0.2715	0.2059	-0.2481	-0.1455	0.0472	0.1284	-0.1518	-0.7218	-0.2972	0.465	0.3389	-0.1958	0.6406	-0.1532	0.358	15.4285	74.8409	19.2131
12	0.0009	-0.0278	0.0054	0.0781	0.0736	0.0313	0.2131	0.133	0.4376	-0.0775	-0.1261	-0.2216	-0.0405	0.0158	-0	0.331	0.0584	0.0204	0.4056	-0.0155	0.283	33.0652	54.6302	24.5615
13	0.0148	0.0064	-0.0145	0.0086	0.0165	0.0259	0.2075	-0.2708	0.5419	-0.0175	-0.2156	-0.1552	-0.2184	-0.1233	-0.0002	0.3118	-0.0479	0.0246	0.3063	-0.0286	0.2872	41.0283	55.0029	22.617
14	0.0553	0.0342	0.0629	0.0191	0.0423	0.0629	0.0576	0.1227	-0.1257	-0.0137	0.0944	0.4044	0.3609	0.0272	0.0173	0.2226	-0.0435	0.0389	0.4111	-0.0249	0.3945	22.0064	52.077	20.3401
15	0.0554	-0.0373	0.0277	0.0339	-0.0453	0.0188	0.0558	0.095	-0.0632	0.4152	-0.3799	0.3488	-0.0638	-0.544	-0.0098	0.2968	0.0066	0.0624	0.3519	-0.1197	0.3435	26.6217	49.5312	21.8571
16	0.0196	-0.0352	-0.0163	0.023	0.0225	-0.0006	0.0413	-0.2363	0.0075	-0.0512	-0.128	-0.1274	0.0777	0.0234	-0.0002	0.3381	0.0384	0.0796	0.4114	-0.1318	0.3991	25.8904	52.2239	30.0197
17	0.7631	0.6319	0.766	0.9067	-0.3984	0.2587	0.0748	-0.1132	0.0349	0.1794	-0.0092	-0.0466	-0.1658	-0.0169	0.0001	0.1949	-0.0107	0.0192	0.1786	-0.0075	0.1515	63.4725	52.1058	66.8262
18	0.6828	-0.1498	0.7025	0.0752	-0.2412	0.9583	0.1576	-0.3158	-0.1459	-0.0992	0.1186	0.1819	0.1459	-0.4028	0.0858	0.2475	-0.0751	-0.0205	0.069	-0.0095	0.2911	53.558	41.6943	51.7813
19	0.2592	0.4888	0.0916	0.5267	-0.1627	0.2444	-0.0594	0.0125	0.0549	0.0436	0.056	0.0673	-0.0659	-0.011	-0	0.1823	-0.0109	-0.0248	0.1856	-0.0163	0.1911	62.9404	56.8127	57.614
20	0.6689	0.0424	0.0547	0.4376	-0.6859	0.9076	0.0335	0.22	0.2267	-0.1562	-0.0995	-0.0443	-0.2008	0.0096	-0	0.2684	-0.0001	-0.0335	0.2012	0.0271	0.2171	77.427	67.2696	50.1497
21	0.168	-0.1749	-0.1315	0.33	0.1131	0.6229	0.0343	-0.0175	-0.0235	-0.4012	-0.2791	-0.5487	-0.2224	0.2313	-0.1863	0.3134	0.0027	0.0869	0.2664	0.0479	0.278	87.9604	58.5616	47.5695
22	0.0321	-0.0149	-0.0658	0.7026	-0.2559	0.3339	-0.0425	0.0024	-0.0014	0.0228	-0.1601	-0.1011	0.0127	-0.0785	-0.004	0.1841	-0.0207	-0.0034	0.1851	-0.0032	0.1933	75.8587	51.8071	62.3439
23	0.2684	-0.0195	0.1541	0.1395	0.3753	0.4393	0.0082	0.044	0.3213	0.034	-0.0093	-0.0747	-0.4141	-0.2939	-0.0161	0.4041	0.1086	-0.0703	0.2108	0	0.4257	29.5749	83.7656	40.0962
24	0.6599	-0.3628	0.3974	0.0618	-0.1739	0.6932	-0.0736	0.0813	0.0804	-0.1648	-0.1323	0.0525	-0.2707	0.0061	-0.2317	0.2853	0.0366	-0.1088	0.1891	0.0477	0.3649	45.5933	76.2807	46.701

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:66)	A	1 - 66
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 67:87)	A	67 - 87
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 88:187)	A	88 - 187
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 188:265)	A	188 - 265
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 266:310)	A	266 - 310
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 7:25)	B	7 - 25
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 26:41)	B	26 - 41
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 42:67)	B	42 - 67
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 68:74)	B	68 - 74
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 75:87)	B	75 - 87
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 88:101)	B	88 - 101
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 102:114)	B	102 - 114
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 115:123)	B	115 - 123
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 124:130)	B	124 - 130
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 131:143)	B	131 - 143
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 144:153)	B	144 - 153
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 1:66)	C	1 - 66
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 67:87)	C	67 - 87
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 88:166)	C	88 - 166
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 167:236)	C	167 - 236
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 237:265)	C	237 - 265
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 266:310)	C	266 - 310
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 6:67)	D	6 - 67
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 68:153)	D	68 - 153

-
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

-
Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD

-
Non-polymers , 5 types, 582 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

-Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD

-Non-polymers , 5 types, 582 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

-
Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD

-
Non-polymers , 5 types, 582 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