PDB-5svc: Mechanism of ATP-Dependent Acetone Carboxylation, Acetone Carboxy...

ID or keywords:

Entry

Database: PDB / ID: 5svc

Title

Mechanism of ATP-Dependent Acetone Carboxylation, Acetone Carboxylase nucleotide-free structure

Components

(Acetone carboxylase ...) x 3

Keywords

LIGASE / Acetone Carboxylase / acetoacetate

Function / homology

Function and homology information

acetone carboxylase / acetone carboxylase activity / cellular detoxification of acetone / 5-oxoprolinase (ATP-hydrolyzing) activity / glutathione metabolic process / ATP binding / cytosol
Similarity search - Function

Biological species

Xanthobacter autotrophicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.7 Å

Authors

Eilers, B.J. / Mus, F. / Alleman, A.B. / Kabasakal, B.V. / Murray, J.W. / Nocek, B.P. / Dubois, J.L. / Peters, J.W.

Funding support

United States, 1items

Citation

Journal: Sci Rep / Year: 2017
Title: Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation.
Authors: Mus, F. / Eilers, B.J. / Alleman, A.B. / Kabasakal, B.V. / Wells, J.N. / Murray, J.W. / Nocek, B.P. / DuBois, J.L. / Peters, J.W.

History

Deposition	Aug 5, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Feb 20, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5svc.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb5svc.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	5svc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5svc_validation.pdf.gz	494.2 KB	Display	wwPDB validaton report
Full document	5svc_full_validation.pdf.gz	548.3 KB	Display
Data in XML	5svc_validation.xml.gz	111.3 KB	Display
Data in CIF	5svc_validation.cif.gz	152.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sv/5svc ftp://data.pdbj.org/pub/pdb/validation_reports/sv/5svc	HTTPS FTP

-
Related structure data

Related structure data	5m45C 5svbC C: citing same article (ref.)
Similar structure data	5m45-2 5m45-1 4gxu-2 23579 6yej-d 30756 6mlm-d 2yfl-d 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: Acetone carboxylase alpha subunit

B: Acetone carboxylase beta subunit

C: Acetone carboxylase gamma subunit

D: Acetone carboxylase alpha subunit

E: Acetone carboxylase beta subunit

F: Acetone carboxylase gamma subunit

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	76.760, 265.159, 122.170
Angle α, β, γ (deg.)	90.00, 92.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Acetone carboxylase ... , 3 types, 6 molecules ADBECF

#1: Protein	Acetone carboxylase alpha subunit Mass: 86440.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (bacteria) Strain: ATCC BAA-1158 / Py2 / Gene: acxB, Xaut_3510 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RM03, acetone carboxylase
#2: Protein	Acetone carboxylase beta subunit Mass: 79793.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (bacteria) Strain: ATCC BAA-1158 / Py2 / Gene: acxA, Xaut_3509 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RM04, acetone carboxylase
#3: Protein	Acetone carboxylase gamma subunit Mass: 19798.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (bacteria) Strain: ATCC BAA-1158 / Py2 / Gene: acxC, Xaut_3511 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RM02, acetone carboxylase

-
Non-polymers , 4 types, 117 molecules

#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.4 Å³/Da / Density % sol: 63.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 12-18%PEG 3350 and 0.2M MgSO4, pH and cryo was the addition of 15% glycerol PH range: 6.3-7.2

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 20, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.7→39 Å / Num. obs: 247620 / % possible obs: 93 % / Redundancy: 4.7 % / CC_1/2: 0.993 / R_merge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.827 / Mean I/σ(I) obs: 1.8 / CC_1/2: 0.725 / % possible all: 93.4

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
Aimless		data scaling
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→38.899 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 29.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2549	12326	4.98 %
R_work	0.2015	-	-
obs	0.2042	247620	93.68 %

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.7→38.899 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25686	0	14	111	25811

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	26342
X-RAY DIFFRACTION	f_angle_d	1.156	35712
X-RAY DIFFRACTION	f_dihedral_angle_d	15.153	15554
X-RAY DIFFRACTION	f_chiral_restr	0.061	3802
X-RAY DIFFRACTION	f_plane_restr	0.007	4672

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 (%)
2.7-2.7307	0.4386	391	0.363	8031	X-RAY DIFFRACTION	95
2.7307-2.7628	0.4099	406	0.3388	7754	X-RAY DIFFRACTION	94
2.7628-2.7965	0.3663	370	0.3291	7653	X-RAY DIFFRACTION	92
2.7965-2.8319	0.3536	406	0.3199	7476	X-RAY DIFFRACTION	88
2.8319-2.8691	0.4057	414	0.3199	7738	X-RAY DIFFRACTION	94
2.8691-2.9084	0.3162	407	0.296	8198	X-RAY DIFFRACTION	97
2.9084-2.9499	0.3737	413	0.2957	8174	X-RAY DIFFRACTION	97
2.9499-2.994	0.3419	427	0.2793	7977	X-RAY DIFFRACTION	97
2.994-3.0407	0.3244	468	0.2684	8072	X-RAY DIFFRACTION	96
3.0407-3.0906	0.3163	400	0.2743	8123	X-RAY DIFFRACTION	97
3.0906-3.1438	0.3429	485	0.266	7911	X-RAY DIFFRACTION	96
3.1438-3.201	0.3105	413	0.2474	8080	X-RAY DIFFRACTION	95
3.201-3.2625	0.3507	416	0.266	7870	X-RAY DIFFRACTION	95
3.2625-3.3291	0.3329	391	0.2592	7909	X-RAY DIFFRACTION	93
3.3291-3.4014	0.292	406	0.2435	7646	X-RAY DIFFRACTION	92
3.4014-3.4805	0.3126	349	0.2363	7383	X-RAY DIFFRACTION	87
3.4805-3.5675	0.3006	406	0.2302	7790	X-RAY DIFFRACTION	93
3.5675-3.6639	0.2423	414	0.2054	8053	X-RAY DIFFRACTION	96
3.6639-3.7716	0.2747	408	0.1977	8028	X-RAY DIFFRACTION	96
3.7716-3.8932	0.2273	391	0.1846	8035	X-RAY DIFFRACTION	96
3.8932-4.0322	0.2397	375	0.1779	8068	X-RAY DIFFRACTION	96
4.0322-4.1935	0.2214	444	0.161	7814	X-RAY DIFFRACTION	94
4.1935-4.3841	0.2105	468	0.1528	7668	X-RAY DIFFRACTION	93
4.3841-4.6149	0.1983	383	0.1464	7191	X-RAY DIFFRACTION	86
4.6149-4.9035	0.1964	447	0.1416	8004	X-RAY DIFFRACTION	95
4.9035-5.2813	0.1921	422	0.1439	7979	X-RAY DIFFRACTION	95
5.2813-5.8112	0.2101	456	0.1486	7807	X-RAY DIFFRACTION	94
5.8112-6.6484	0.2098	387	0.159	7550	X-RAY DIFFRACTION	90
6.6484-8.3626	0.1683	365	0.1423	7717	X-RAY DIFFRACTION	91
8.3626-38.9029	0.178	398	0.1464	7595	X-RAY DIFFRACTION	91

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	1.1225	-0.0121	-0.3271	1.3657	-0.2557	1.7939	-0.0821	0.232	0.1924	-0.3119	-0.0431	0.3476	-0.2527	-0.243	0.0931	0.2138	0.0618	-0.0559	0.7644	-0.064	0.4228	-56.2438	-43.151	-48.6399
2	0.0344	0.1247	0.26	0.8727	0.0169	0.4184	-0.051	0.0166	0.0379	-0.0419	-0.0138	0.1531	-0.0429	-0.4904	0.0519	0.2333	0.0401	-0.0169	0.6412	-0.0281	0.35	-47.5533	-51.5983	-36.5982
3	0.1948	0.0739	-0.0699	0.7531	0.0794	0.2048	0.0069	0.0002	0.0176	-0.0254	-0.0539	-0.1002	-0.0005	-0.0969	0.0452	0.2179	0.0008	-0.011	0.6721	-0.0166	0.3511	-23.3979	-44.8362	-37.2232
4	-0.0371	0.3288	-0.3105	2.4043	-1.4051	1.769	0.0759	-0.1933	0.0659	0.1208	-0.1139	-0.3189	-0.1561	0.0926	0.0928	0.1859	-0.0084	-0.0323	0.5108	0.06	0.4488	-12.9251	-33.0713	-33.0027
5	0.9811	0.3147	-0.0363	2.9128	0.52	0.8657	-0.1109	0.1013	0.0858	-0.235	0.1909	-0.5997	-0.0722	0.2267	-0.1442	0.1714	0.0449	0.03	0.5589	0.0708	0.4733	-4.5	-36.9987	-49.8265
6	2.5919	0.8934	-2.0462	1.2178	-1.4396	2.1521	-0.113	0.2446	-0.2636	-0.2546	-0.0728	-0.2151	0.1761	-0.1239	0.1768	0.3408	-0.076	0.0227	0.5132	-0.029	0.2729	-22.5012	-61.7657	-56.9493
7	0.6673	-0.7632	-0.4578	1.7301	0.5711	0.0963	-0.0286	-0.272	0.1117	0.044	0.0587	-0.0327	-0.2101	-0.0837	-0.0184	0.4137	0.0379	-0.0304	0.6274	-0.1014	0.316	-39.8721	-15.9696	-15.5728
8	0.3409	-0.135	-0.1258	3.1783	-0.0244	1.132	0.0685	0.0497	0.0327	-0.2896	-0.0964	0.1822	-0.2606	0.0243	0.0382	0.4568	0.0944	-0.0244	0.8068	-0.135	0.3741	-52.3177	-11.7882	-24.6233
9	0.3051	-0.3235	-0.0536	3.0511	0.7154	0.8245	-0.0091	-0.0026	-0.0193	-0.0989	-0.1435	0.7222	-0.3115	-0.1707	0.1308	0.3398	0.0855	-0.052	0.865	-0.1627	0.5317	-62.8273	-18.6813	-20.7042
10	7.5911	3.9903	-4.773	7.4801	-2.8392	6.1292	0.0765	-0.6441	0.8734	0.5598	0.1264	0.4048	-0.2756	-0.4762	-0.17	0.392	0.0513	-0.0274	0.4185	-0.0873	0.2947	-30.84	-15.504	-48.768
11	5.7751	0.706	-0.2587	1.4083	0.5998	0.2931	-0.0874	0.636	0.6326	-0.0956	0.1453	-0.0125	-0.1147	0.0496	-0.0181	0.4124	0.1538	-0.0111	0.6606	0.0439	0.2993	-25.2176	-17.9209	-62.2966
12	1.9506	-0.93	1.6535	3.4257	-2.0517	1.9327	0.1598	0.4056	0.1162	-0.5449	-0.1148	-0.428	0.1285	0.2359	0.0796	0.646	0.1268	0.1549	0.1717	0.1057	0.4764	-16.3166	-23.7747	-69.3791
13	4.6374	-1.8481	-0.3559	7.3691	-3.9344	4.0599	0.0423	0.1865	0.287	-0.8073	-0.3459	-0.764	0.3492	-0.5673	0.2752	0.371	0.0385	0.0831	0.5223	0.0398	0.3102	-12.0949	-30.8643	-66.7334
14	3.5022	-0.4276	-0.0908	3.2852	-1.4748	3.6171	0.0593	-0.1551	0.1778	-0.2905	-0.2132	-0.7109	-0.1703	0.6491	0.1535	0.2515	-0.0587	0.0359	0.2524	0.0015	0.4034	-5.7065	-37.7431	-48.3399
15	0.137	-0.4673	0.3035	1.969	-1.2037	0.7685	0.1883	-0.0321	0.365	-0.4755	-0.4239	-0.6559	0.0817	0.6189	0.1656	0.3445	0.0403	0.0954	0.6262	0.0243	0.4014	-15.9533	-42.4995	-59.2852
16	6.9975	0.9364	-6.8367	1.749	-1.0818	8.6343	0.2758	0.9576	0.1216	-0.7461	-0.0761	0.279	-0.2189	-0.7525	-0.2854	0.5288	0.1104	-0.0063	0.5168	0.1259	0.399	-29.9246	-26.6131	-73.0717
17	0.6521	0.1425	-0.0757	1.5613	-0.1047	1.8215	0.0518	-0.3982	-0.0751	0.3022	-0.0719	0.3589	0.1219	-0.255	0.0194	0.2688	-0.0831	0.0578	0.7321	-0.0109	0.4115	-57.8851	-91.0604	-14.277
18	0.2278	0.2451	0.0786	1.4141	0.3659	0.2137	0.0363	0.0599	-0.1497	0.0647	-0.1371	0.1039	-0.0045	-0.1765	0.0933	0.2397	-0.0724	0.0242	0.6373	-0.0114	0.329	-46.0141	-81.0789	-24.6569
19	0.1186	-0.1297	0.3484	0.7175	-0.5734	1.1242	0.0145	-0.0655	-0.0002	0.072	-0.0474	0.2123	0.065	-0.1306	0.018	0.2394	-0.0805	0.0168	0.5431	-0.0754	0.388	-50.7689	-84.605	-26.5165
20	0.81	0.3128	0.1667	1.5807	-0.5338	0.2133	0.0739	-0.3856	-0.0205	0.28	-0.1727	0.0104	-0.0045	0.0878	0.1048	0.3331	-0.0771	0.0024	0.7624	-0.0082	0.3173	-27.4351	-83.9483	-11.0348
21	-0.0017	0.0172	0.1955	0.572	0.0708	0.0811	0.035	-0.1462	-0.0519	0.024	-0.0849	-0.0968	-0.0164	-0.0033	0.0538	0.2456	-0.0328	0.0282	0.665	0.0302	0.3738	-23.0762	-91.5778	-26.8708
22	0.2578	0.2926	0.0283	1.1523	-0.8851	0.8927	-0.1025	-0.0315	-0.1771	-0.1322	-0.0734	-0.3183	0.1349	0.049	0.214	0.2273	0.0087	0.0467	0.6432	0.0806	0.4329	-13.505	-101.4421	-26.0507
23	0.8439	-0.1271	0.0565	2.0843	0.2651	0.8638	-0.0641	-0.1086	-0.1314	0.1411	-0.0175	-0.4462	0.0604	0.1679	0.0482	0.2314	-0.0824	-0.0185	0.7712	0.0876	0.4738	-6.4778	-97.5503	-8.5216
24	1.7453	-0.4174	1.4926	0.7393	-0.6646	1.3168	-0.0203	-0.7245	0.1113	0.3302	-0.0339	-0.1152	-0.1503	-0.3946	0.041	0.5258	-0.0574	-0.046	0.5869	-0.0219	0.2824	-24.7986	-72.6443	-3.0476
25	0.4347	0.5595	0.3776	2.0098	0.6262	0.0435	-0.0197	0.1896	-0.0567	-0.0245	-0.0081	-0.0018	0.1783	0.019	0.0256	0.4052	-0.0367	0.0609	0.5153	-0.026	0.2899	-39.043	-118.4304	-45.7017
26	0.32	0.2393	0.0402	3.2243	0.8818	1.5437	0.0822	-0.0504	-0.063	0.6829	-0.1209	0.409	0.379	0.0518	0.0295	0.6394	-0.0827	0.1188	0.5781	-0.0861	0.4649	-52.2715	-122.4596	-37.7607
27	0.0936	-0.2035	0.0849	2.6168	1.4242	0.6593	-0.0821	-0.1423	-0.0668	0.2875	-0.2462	0.8427	0.4255	-0.0475	0.251	0.4423	-0.1125	0.1348	0.716	-0.0327	0.6542	-62.3682	-115.5147	-42.6166
28	7.7285	-0.4093	1.5025	2.9139	-2.6541	2.6385	0.0845	0.6476	-0.7196	0.0033	0.2895	0.0157	0.7604	-1.0461	-0.3476	0.4795	-0.086	0.0695	0.4879	0.0005	0.4115	-30.4329	-120.8149	-9.5113
29	5.6064	-1.1284	-0.8942	2.2786	-1.0285	2.4982	0.2034	0.0131	-0.6684	-0.041	-0.1185	0.003	0.0116	-0.2241	-0.0902	0.4075	-0.1539	-0.0075	0.5974	0.0375	0.3519	-33.6337	-116.4752	-5.6842
30	1.5005	0.6798	0.2863	2.6847	-0.4611	1.7853	-0.0668	-0.5693	-0.3276	0.5021	-0.4184	-0.417	-0.4499	0.4136	0.3835	0.6012	-0.1315	-0.0119	0.4306	0.164	0.4173	-20.5322	-112.3266	9.1339
31	1.9132	2.1857	-0.5299	4.2644	-2.3073	1.7798	0.2362	-0.2893	-0.3227	0.5596	-0.0025	-0.2858	-0.3688	0.1532	-0.1807	0.4669	-0.1131	-0.087	0.8463	0.1542	0.4207	-15.5211	-103.5326	7.6137
32	2.5927	-1.1824	2.854	2.8692	-0.0944	3.7619	0.2251	0.3947	-0.2252	0.1877	0.2675	-0.7251	0.2966	0.7536	-0.1311	0.2779	0.0081	-0.0738	0.7435	0.0922	0.5833	-3.1634	-95.7213	-10.8168
33	2.5338	0.584	-0.6312	2.7282	-0.2704	2.7353	0.001	-0.385	-0.0561	0.4052	-0.35	-0.3264	0.1232	0.2799	0.3436	0.2744	-0.0415	-0.0625	0.611	0.0788	0.3903	-12.5647	-95.5276	-6.67
34	5.5221	-0.7829	4.9064	0.5353	-1.3416	5.4355	0.2586	-0.8236	-0.4563	0.3186	0.0051	0.2926	-0.0534	-0.9573	-0.3425	0.5451	-0.2365	0.0637	0.6716	0.1482	0.4995	-33.8921	-107.6805	12.3749

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 282 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 283 through 609 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 610 through 657 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 658 through 724 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 725 through 776 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 8 through 367 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 368 through 555 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 556 through 717 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 26 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 27 through 54 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 55 through 74 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 75 through 91 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 92 through 134 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 135 through 149 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 150 through 167 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 14 through 78 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 79 through 195 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 196 through 282 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 283 through 363 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 364 through 609 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 610 through 657 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 658 through 724 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 725 through 776 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 8 through 367 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 368 through 555 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 556 through 717 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 2 through 17 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 18 through 44 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 45 through 74 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 75 through 91 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 92 through 104 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 105 through 149 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 150 through 167 )

-
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

-
Acetone carboxylase ... , 3 types, 6 molecules ADBECF

-
Non-polymers , 4 types, 117 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Acetone carboxylase ... , 3 types, 6 molecules ADBECF

-Non-polymers , 4 types, 117 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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

-
Acetone carboxylase ... , 3 types, 6 molecules ADBECF

-
Non-polymers , 4 types, 117 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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