PDB-5ku6: Crystal structure for the complex of human carbonic anhydrase IV ...

ID or keywords:

Entry

Database: PDB / ID: 5ku6

Title

Crystal structure for the complex of human carbonic anhydrase IV and methazolamide

Components

Carbonic anhydrase 4

Keywords

lyase/lyase inhibitor /

Carbonic anhydrase / Intrinsic thermodynamics /

lyase /

inhibitor / lyase-lyase inhibitor complex

Function / homology

Function and homology information

bicarbonate transport / transport vesicle membrane /

endoplasmic reticulum-Golgi intermediate compartment /

rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / brush border membrane /

carbonic anhydrase /

carbonate dehydratase activity /

trans-Golgi network ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Chen, Z. / Waheed, A. / Di Cera, E. / Sly, W.S.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	HL049413	United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	HL073813	United States

Citation

Journal: Eur. Biophys. J. / Year: 2018
Title: Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV.
Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / ...

History

Deposition	Jul 12, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2017	Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2	Feb 6, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Mar 23, 2022	Group: Author supporting evidence / Database references / Derived calculations Category: database_2 / pdbx_audit_support / 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_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ku6.cif.gz	468.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ku6.ent.gz	387.3 KB	Display	PDB format
PDBx/mmJSON format	5ku6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ku/5ku6 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5ku6	HTTPS FTP

-
Related structure data

Related structure data	5ipzC 5jn8C 5jn9C 5jnaC 5jncC 1zncS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jna-1 5jn8-1 5jn8-3 5jnc-1 3gjb-2 5jna-3 5jnc-3 5jn9-1 1trg-d 2xbx-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

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	#49 - Jan 2004 Carbonic Anhydrase similarity (1)

Deposited unit

A: Carbonic anhydrase 4

B: Carbonic anhydrase 4

C: Carbonic anhydrase 4

D: Carbonic anhydrase 4

hetero molecules

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

1

A: Carbonic anhydrase 4

hetero molecules

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

2

B: Carbonic anhydrase 4

hetero molecules

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

3

C: Carbonic anhydrase 4

hetero molecules

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

4

D: Carbonic anhydrase 4

hetero molecules

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

5

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	64.965, 123.698, 151.367
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 4 molecules ABCD

#1: Protein	Carbonic anhydrase 4 / / Carbonate dehydratase IV / Carbonic anhydrase IV / CA-IV Mass: 30364.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22748, carbonic anhydrase

-
Non-polymers , 6 types, 939 molecules

#2: Chemical	ChemComp-MZM / N-(3-methyl-5-sulfamoyl-1,3,4-thiadiazol-2(3H)-ylidene)acetamide / Methazolamide / Methazolamide Mass: 236.272 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₈N₄O₃S₂ / Comment: inhibitor*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.5 Å³/Da / Density % sol: 50.87 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Na acetate, 200 mM AmSO4 and 23% PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2015
Radiation	Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.8→40 Å / Num. obs: 110310 / % possible obs: 97.3 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 4.4 % / R_merge(I) obs: 0.089 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.422 / Mean I/σ(I) obs: 2.1 / % possible all: 94.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ZNC

1znc

Resolution: 1.8→95.78 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.939 / SU B: 6.494 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21585	5481	5 %	RANDOM
R_work	0.18416	-	-	-
obs	0.18574	104356	96.85 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.503 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	0 Å²	0 Å²
2-	-	-0.06 Å²	0 Å²
3-	-	-	0.13 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→95.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8360	0	142	915	9417

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	8698
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.97	11755
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.271	5	1027
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.512	24.938	403
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.423	15	1551
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.137	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1253
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	6500
X-RAY DIFFRACTION	r_gen_planes_other
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	0.437	1.5	5202
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.839	2	8403
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.528	3	3496
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.545	4.5	3350
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

LS refinement shell

Resolution: 1.801→1.848 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	413	-
R_work	0.323	7269	-
obs	-	-	92.67 %

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	2.0894	-1.0446	-0.8245	3.9794	1.1274	3.6041	-0.0422	-0.0454	-0.3154	0.0864	0.1171	-0.1932	0.2446	0.2052	-0.0749	0.1294	0.0203	-0.0032	0.1576	0.0105	0.163	38.8256	-6.8171	16.7461
2	3.9842	-1.1904	-0.4223	3.1789	0.3972	2.1602	-0.0712	-0.5794	-0.0344	0.2804	0.1483	0.1988	-0.0044	-0.0739	-0.0772	0.1428	-0.0152	0.04	0.1031	0.0082	0.0655	23.0035	6.1536	26.8879
3	2.4826	-2.0167	-1.4597	3.5378	1.9102	1.4802	-0.0227	-0.0981	0.3034	-0.0474	0.0904	-0.1938	-0.1609	0.0898	-0.0677	0.1251	-0.0278	-0.0396	0.1518	0.0004	0.1125	32.7513	21.2106	12.5218
4	1.8765	-0.6341	-0.6305	5.124	2.5038	2.8724	-0.0432	-0.0827	0.2104	-0.0264	0.1093	-0.2176	-0.1248	0.2221	-0.0662	0.0595	-0.0149	-0.0147	0.0811	0.0337	0.0555	32.1286	16.8292	15.5413
5	7.6742	2.3539	-1.5645	3.3526	1.2039	5.6297	-0.084	0.5498	-0.1144	-0.394	0.1122	0.1971	0.1713	-0.227	-0.0282	0.1238	-0.001	-0.0209	0.0888	0.0297	0.0826	19.5449	3.6606	13.7612
6	2.725	2.1751	1.8526	5.4713	3.7165	5.1722	0.0422	-0.2213	0.0456	0.3161	0.0253	-0.1308	0.0069	0.0507	-0.0674	0.0607	0.0133	0.0156	0.057	0.0156	0.0577	30.1909	16.1241	21.111
7	3.7076	0.2279	0.2886	1.7314	0.3068	1.3653	0.0388	0.1903	0.3495	-0.1609	-0.0412	-0.0539	-0.1232	0.0995	0.0024	0.1536	-0.0157	0.0086	0.1356	0.0143	0.0645	34.5316	13.1262	-0.385
8	3.2509	1.2706	-5.2173	0.8407	-1.7813	8.6077	0.2041	0.4253	0.3028	-0.1833	0.0818	0.3205	-0.5095	-0.7085	-0.2859	0.2716	0.0513	-0.078	0.1615	-0.0085	0.2346	21.451	22.106	11.9687
9	1.1458	-0.6934	-0.728	1.368	0.8308	3.13	0.0501	0.0274	-0.0055	-0.0066	-0.013	-0.0167	0.013	0.1181	-0.0371	0.0402	-0.0321	-0.0032	0.0433	0.0104	0.0617	31.2377	6.3093	10.6001
10	3.2413	-2.7762	-2.1432	5.2607	0.2262	3.3408	-0.3323	-0.178	-0.3839	0.5893	0.1162	0.7133	0.208	-0.1146	0.216	0.1245	-0.0382	0.0673	0.1132	-0.0074	0.1685	21.1116	6.319	26.1491
11	0.9482	0.281	3.6466	5.7697	0.7924	14.3807	-0.2284	0.1871	0.0435	0.2098	0.2572	-0.7049	-0.9169	0.9244	-0.0288	0.1276	-0.0463	-0.0202	0.2603	-0.1024	0.2901	35.6185	5.7873	-21.3238
12	2.8939	1.0037	-0.1078	3.2516	-0.5938	2.21	-0.0952	0.4388	0.0577	-0.3098	0.0528	0.1278	0.0686	-0.0823	0.0424	0.0822	0.0169	-0.0295	0.0844	-0.0145	0.0719	23.8284	-5.2481	-30.8916
13	5.4956	-2.0199	2.2391	3.959	-0.7141	2.6649	0.1486	0.1657	-0.5715	-0.0792	-0.0045	0.331	0.2296	0.0413	-0.1441	0.2057	-0.0114	0.0513	0.1159	-0.0161	0.1861	20.7995	-25.9249	-20.9418
14	1.6465	1.2934	1.0797	2.7489	1.8677	1.3175	-0.0043	0.156	-0.4654	0.0409	0.2787	-0.3566	0.0572	0.2148	-0.2744	0.2324	0.0427	0.0182	0.1441	0.0154	0.2043	35.7965	-19.8222	-18.3316
15	1.1126	0.8554	1.2356	1.9377	0.3348	1.685	0.0114	-0.0234	-0.0127	0.0892	0.0207	0.0045	0.0308	-0.0339	-0.0321	0.1251	0.0178	-0.0065	0.0557	0.0131	0.0483	25.9032	-11.4376	-17.6923
16	2.297	-0.4371	-0.1113	3.0909	1.7869	5.5245	0.0356	0.0402	-0.0648	-0.0372	-0.0315	0.0658	0.046	-0.2312	-0.0041	0.0648	-0.0114	-0.0308	0.0126	0.006	0.1915	26.5723	-17.7951	-18.353
17	1.9072	0.507	1.896	1.6084	0.0381	2.9915	0.1587	-0.2252	-0.2168	0.233	-0.057	0.0105	0.3008	-0.0252	-0.1016	0.1343	0.0516	0.0172	0.1202	-0.0121	0.155	30.5535	-16.3727	-13.66
18	2.1551	0.8413	2.2853	1.0349	0.8299	6.4898	0.0725	-0.2785	-0.1016	0.1782	-0.2536	0.1387	0.015	-0.7335	0.1811	0.1326	-0.0056	0.0043	0.1246	-0.0501	0.1367	22.6484	-13.8262	-14.6315
19	5.777	1.2978	1.2011	2.6804	0.8206	0.9587	0.0684	-0.1394	0.0725	0.0626	-0.0515	-0.0938	-0.048	0.2851	-0.0169	0.0659	-0.0205	-0.0279	0.1864	-0.0149	0.0293	36.1384	-3.0271	-7.4144
20	2.4408	0.5402	1.3225	2.0146	0.7408	3.0585	-0.1684	0.0286	0.1867	-0.1378	-0.0344	0.274	-0.2606	-0.0904	0.2028	0.0697	0.0197	0.014	0.056	0.0077	0.0852	24.5271	-4.7612	-22.6164
21	5.9889	-0.1896	-1.2264	2.7671	-2.4967	10.0751	0.122	0.0096	0.6555	-0.0542	-0.1442	-0.4019	-0.6843	0.7704	0.0222	0.16	-0.0457	-0.0099	0.1725	-0.0038	0.2038	20.2494	20.9212	-18.0121
22	4.2962	0.7943	0.3287	2.5581	0.3284	2.0087	0.0771	-0.3005	-0.3911	0.1982	-0.1119	0.1739	0.2056	-0.244	0.0348	0.1157	0.0068	0.0316	0.1108	0.0285	0.1023	2.5404	3.9256	-11.6108
23	2.8912	0.1301	-1.1345	0.6406	-0.3275	1.5873	0.0256	0.005	0.0694	0.0234	-0.0227	0.2418	-0.1258	-0.2117	-0.0029	0.1086	0.0182	-0.0102	0.1039	-0.0319	0.1081	-3.8583	17.9748	-24.085
24	3.6337	-0.6462	-1.7646	1.5566	0.0161	3.4559	0.1319	-0.1036	0.0469	0.0405	-0.0363	0.0493	-0.0486	-0.0941	-0.0956	0.058	-0.0414	-0.0249	0.0511	-0.0055	0.0638	-0.8616	10.6176	-17.8142
25	15.4137	-0.9921	-12.1663	0.1042	1.3941	19.3199	0.0223	-0.5014	0.1374	0.0255	0.0327	-0.0111	0.121	0.1732	-0.0549	0.207	-0.0322	0.0347	0.1948	-0.0052	0.2218	-7.4695	13.5642	-2.3676
26	1.1622	0.5059	-0.3847	1.2887	-1.7912	2.8699	-0.0638	0.2935	-0.1852	-0.2676	0.0402	-0.0123	0.2494	-0.1326	0.0235	0.1496	0.0687	-0.026	0.2048	-0.0663	0.1464	-0.1893	11.8523	-32.7594
27	3.6975	2.0771	-0.3419	4.2525	-0.909	1.7556	-0.1225	0.2817	0.0045	-0.3496	0.163	0.2788	0.0521	-0.2935	-0.0404	0.1286	0.0509	0.0049	0.154	-0.0359	0.0856	-1.8245	20.3074	-32.955
28	8.6257	-4.906	0.2154	5.1108	-5.3085	15.121	0.1416	0.2825	-0.8753	-0.4967	0.1443	0.6069	0.7045	-0.7353	-0.2859	0.1183	-0.0695	-0.0284	0.1049	-0.0608	0.2223	-7.0754	0.4953	-21.7298
29	2.3511	1.1209	-1.4951	1.3317	-1.4038	4.1021	-0.0494	0.052	-0.0356	-0.0241	0.0221	0.0234	0.0476	-0.1136	0.0273	0.0192	0.0206	-0.0035	0.0315	-0.0134	0.08	5.7204	13.8432	-24.4607
30	3.0073	0.8879	-0.4747	2.5214	-0.9754	2.5062	-0.022	-0.1401	-0.2751	0.0931	-0.1159	-0.1701	0.0474	0.1618	0.1379	0.0572	0.0172	0.0024	0.0542	-0.021	0.0781	10.4591	10.435	-18.2114
31	9.8321	2.2586	3.0991	2.2193	-1.7968	11.0594	0.3595	0.4461	-0.9831	-0.163	-0.1717	-0.5247	0.8853	1.2925	-0.1878	0.2249	0.1044	-0.0004	0.2355	-0.0615	0.2731	19.6563	-23.8433	18.6906
32	2.911	0.2102	0.0921	2.5136	-0.2874	2.3977	0.1267	0.5409	0.1092	-0.6185	-0.1766	-0.0081	-0.0774	0.0583	0.0499	0.1906	0.0385	-0.0024	0.2176	0.0164	0.0508	7.0772	-6.742	10.1714
33	2.6526	-1.9443	0.9061	2.942	-0.8121	1.2108	-0.0044	0.015	-0.0797	-0.0074	-0.0044	0.2318	-0.0413	-0.1672	0.0088	0.1065	-0.0174	-0.0158	0.0977	-0.0412	0.1042	-7.1344	-14.6247	26.2519
34	3.3771	-2.0884	1.6148	3.2327	-1.4743	5.163	0.0591	0.1307	-0.3475	-0.0218	0.1194	0.4119	0.1639	-0.2211	-0.1784	0.0474	-0.0106	-0.014	0.0692	-0.037	0.1398	-11.1054	-16.4892	19.7169
35	2.0052	-1.1972	0.5855	1.1533	-1.0343	1.3071	0.0651	0.1364	-0.1369	-0.0089	-0.0496	0.0391	-0.024	0.0424	-0.0155	0.0604	0.0201	0.012	0.0758	-0.0284	0.0554	4.0244	-11.5161	22.4248
36	2.8457	0.7801	3.7744	1.317	2.0731	9.2961	-0.0176	0.1808	-0.0221	-0.1615	-0.001	0.0649	-0.0882	-0.0485	0.0186	0.0772	0.0199	0.0059	0.0402	0.0145	0.102	-2.9447	-9.8807	19.6786
37	4.4634	-2.4154	-1.2994	7.1024	1.2136	2.4067	0.0741	-0.1778	-0.0862	0.2686	-0.0333	0.0658	0.1611	-0.0408	-0.0407	0.099	-0.0287	-0.0144	0.0851	0.0111	0.0651	2.0191	-22.9241	37.1469
38	1.2749	0.8329	-2.0267	5.8189	-4.419	5.5288	0.1235	-0.1531	0.2368	0.8435	0.0602	0.2615	-0.8274	-0.0612	-0.1837	0.2023	0.05	-0.0691	0.1971	-0.085	0.2194	-6.3849	-4.0096	28.2969
39	2.3214	-0.9034	1.4041	0.8731	-0.3064	5.6875	0.0053	0.0968	-0.1037	-0.0692	-0.0606	0.053	-0.1832	-0.0785	0.0553	0.0353	-0.0168	0.0011	0.052	0.0178	0.0767	2.975	-9.8493	19.483
40	2.0307	-1.1915	1.0107	2.0643	-1.0701	2.5675	0.0895	0.1395	-0.0552	-0.1415	-0.0825	-0.0142	0.1753	0.244	-0.0069	0.0414	-0.0159	0.0048	0.0726	-0.0337	0.0693	11.4755	-15.2381	24.8552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 15
2	X-RAY DIFFRACTION	2	A	16 - 41
3	X-RAY DIFFRACTION	3	A	42 - 69
4	X-RAY DIFFRACTION	4	A	70 - 101
5	X-RAY DIFFRACTION	5	A	102 - 112
6	X-RAY DIFFRACTION	6	A	113 - 149
7	X-RAY DIFFRACTION	7	A	150 - 178
8	X-RAY DIFFRACTION	8	A	179 - 193
9	X-RAY DIFFRACTION	9	A	194 - 244
10	X-RAY DIFFRACTION	10	A	245 - 259
11	X-RAY DIFFRACTION	11	B	4 - 15
12	X-RAY DIFFRACTION	12	B	16 - 35
13	X-RAY DIFFRACTION	13	B	36 - 55
14	X-RAY DIFFRACTION	14	B	56 - 86
15	X-RAY DIFFRACTION	15	B	87 - 125
16	X-RAY DIFFRACTION	16	B	126 - 156
17	X-RAY DIFFRACTION	17	B	157 - 204
18	X-RAY DIFFRACTION	18	B	205 - 222
19	X-RAY DIFFRACTION	19	B	223 - 233
20	X-RAY DIFFRACTION	20	B	236 - 259
21	X-RAY DIFFRACTION	21	C	4 - 15
22	X-RAY DIFFRACTION	22	C	16 - 46
23	X-RAY DIFFRACTION	23	C	47 - 102
24	X-RAY DIFFRACTION	24	C	103 - 130
25	X-RAY DIFFRACTION	25	C	131 - 140
26	X-RAY DIFFRACTION	26	C	141 - 161
27	X-RAY DIFFRACTION	27	C	162 - 188
28	X-RAY DIFFRACTION	28	C	189 - 192
29	X-RAY DIFFRACTION	29	C	193 - 233
30	X-RAY DIFFRACTION	30	C	236 - 259
31	X-RAY DIFFRACTION	31	D	4 - 15
32	X-RAY DIFFRACTION	32	D	16 - 41
33	X-RAY DIFFRACTION	33	D	42 - 68
34	X-RAY DIFFRACTION	34	D	69 - 91
35	X-RAY DIFFRACTION	35	D	92 - 128
36	X-RAY DIFFRACTION	36	D	129 - 154
37	X-RAY DIFFRACTION	37	D	155 - 178
38	X-RAY DIFFRACTION	38	D	179 - 192
39	X-RAY DIFFRACTION	39	D	193 - 220
40	X-RAY DIFFRACTION	40	D	221 - 259

-
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

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 939 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 6 types, 939 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 6 types, 939 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