PDB-4c6x: Crystal structure of M. tuberculosis C171Q KasA in complex with t...

ID or keywords:

Entry

Database: PDB / ID: 4c6x

Title

Crystal structure of M. tuberculosis C171Q KasA in complex with thiolactomycin (TLM)

Components

3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1

Keywords

TRANSFERASE / KASA / KAS ENZYME / CONDENSING ENZYME / TYPE 2 FATTY ACID BIOSYNTHESIS / MYCOLIC ACID SYNTHESIS

Function / homology

Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / : / Chem-M7U / THIOLACTOMYCIN / :

Function and homology information

Biological species

MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Schiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for the Recognition of Mycolic Acid Precursors by Kasa, a Condensing Enzyme and Drug Target from Mycobacterium Tuberculosis
Authors: Schiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C.

History

Deposition	Sep 19, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2013	Group: Database references
Revision 1.2	Oct 23, 2013	Group: Database references
Revision 1.3	Dec 11, 2013	Group: Database references
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	4c6x.cif.gz	337.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4c6x.ent.gz	274 KB	Display	PDB format
PDBx/mmJSON format	4c6x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4c6x_validation.pdf.gz	925.6 KB	Display	wwPDB validaton report
Full document	4c6x_full_validation.pdf.gz	933.2 KB	Display
Data in XML	4c6x_validation.xml.gz	39.7 KB	Display
Data in CIF	4c6x_validation.cif.gz	60.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c6/4c6x ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c6x	HTTPS FTP

-
Related structure data

Related structure data	4c6uC 4c6vC 4c6wC 4c6zC 4c70C 4c71C 4c72C 4c73C 2wggS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4c71-d 4c73-d 2wgf-1 2wgg-3 2wgg-1 5w2p-1 2wgg-4 6y2j-4 2wgf-4 3o04-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1

B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1

hetero molecules

93.9 kDa, 2 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)	74.298, 89.323, 183.005
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 1 types, 2 molecules AB

#1: Protein	3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 / BETA-KETOACYL ACP SYNTHASE Mass: 45845.676 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria) Plasmid: PFPCA1 / Production host: MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155 References: UniProt: I6Y8T4, beta-ketoacyl-[acyl-carrier-protein] synthase I

#1: Protein

3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 / BETA-KETOACYL ACP SYNTHASE

Mass: 45845.676 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
Plasmid: PFPCA1 / Production host:

MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155
References: UniProt: I6Y8T4, beta-ketoacyl-[acyl-carrier-protein] synthase I

-
Non-polymers , 6 types, 768 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-TLM / THIOLACTOMYCIN / 4-HYDROXY-3,5-DIMETHYL-5-(2-METHYL-BUTA-1,3-DIENYL)-5H-THIOPHEN-2-ONE Mass: 210.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₄O₂S
#5: Chemical	ChemComp-M7U / (2R)-2-(hexadecanoyloxy)-3-{[(10R)-10-methyloctadecanoyl]oxy}propyl phosphate Mass: 690.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₈H₇₅O₈P
#6: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 760 / 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: 3.5 Å³/Da / Density % sol: 64.91 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 0.1 M HEPES PH 7.5, 30% PEG 400

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
Detector	Type: MARRESEARCH / Detector: CCD / Date: Sep 13, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.95→48.45 Å / Num. obs: 87684 / % possible obs: 98.3 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.95→2.06 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 3.7 / % possible all: 97

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WGG

2wgg

Resolution: 1.95→91.5 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.949 / SU B: 5.016 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17336	4387	5 %	RANDOM
R_work	0.13818	-	-	-
obs	0.13993	83089	97.9 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 19.803 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0 Å²
2-	-	1.99 Å²	0 Å²
3-	-	-	-1.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→91.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6066	0	143	760	6969

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6516
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.635	1.973	8881
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.564	5	888
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.595	23.684	266
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.998	15	1000
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.914	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	983
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	5045
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	1.497	1.5	4204
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.176	2	6725
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.875	3	2312
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.775	4.5	2126
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: 1.951→2.002 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.234	341	-
R_work	0.205	5936	-
obs	-	-	96.23 %

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	0.9677	0.1754	-0.0737	0.8124	0.1024	0.6884	-0.0124	0.0157	-0.1493	-0.0306	-0.0126	-0.0812	0.1416	0.0945	0.025	0.0337	0.0189	0.0044	0.0225	0.0133	0.0448	6.3034	-32.7127	10.4323
2	0.3164	0.5804	-0.5974	1.1178	-1.3985	3.9066	-0.0179	-0.086	-0.1309	-0.0478	-0.1561	-0.1925	0.4314	0.2396	0.1739	0.1593	0.0322	0.0157	0.0912	0.0659	0.1457	1.9589	-43.2899	25.898
3	5.9501	2.0451	0.3713	1.6815	0.1744	1.5506	0.0015	-0.2016	-0.1795	0.127	-0.0551	-0.2123	0.2298	0.212	0.0536	0.0839	0.0516	-0.0317	0.0863	0.0361	0.075	12.7128	-33.3665	26.8986
4	1.4639	0.5911	0.1557	0.4333	0.214	0.8033	0.0243	-0.0871	-0.0735	0.1014	-0.0019	-0.0159	0.1109	-0.0297	-0.0224	0.0811	0.0011	-0.0135	0.038	0.0315	0.0616	-4.0961	-32.7156	31.7399
5	0.3449	0.0788	-0.3286	0.3976	0.0356	1.0962	0.0437	-0.095	-0.0018	0.0451	-0.0447	-0.0682	-0.0286	0.0507	0.0011	0.0446	0.0081	-0.011	0.0831	0.0034	0.0712	3.3569	-18.9779	23.4736
6	0.4034	0.0224	-0.1433	0.4903	0.0743	0.4825	-0.0017	0.0362	-0.0417	-0.0399	-0.0205	0.0082	0.0398	0.0048	0.0222	0.0423	0.0077	-0.0037	0.0382	0.0003	0.0417	-0.1595	-28.376	9.7568
7	3.9527	-2.1901	-0.1189	4.4828	-0.6872	5.1404	0.0155	-0.1061	0.0457	0.1427	-0.0242	-0.2974	-0.1079	0.4836	0.0087	0.0139	-0.032	-0.0226	0.1377	0.0106	0.1139	23.3453	-19.2524	21.8185
8	0.6529	-0.1211	-0.1065	0.5275	0.1726	0.5465	0.0262	0.0536	0.0606	-0.0622	-0.0292	-0.0315	-0.048	0.0381	0.003	0.0416	0.0086	0.0028	0.0561	0.0143	0.0561	4.2213	-16.5442	5.6614
9	0.9563	-0.0259	-0.207	0.5167	0.3395	0.8093	0.0255	0.0273	0.0034	-0.0973	0.0052	-0.0342	-0.048	0.1012	-0.0308	0.0377	0.008	0.0123	0.0551	0.0177	0.0573	9.4792	-19.3678	2.1902
10	0.963	0.2127	0.022	1.016	0.0601	0.8441	-0.0004	-0.1383	0.1166	0.1441	-0.0414	0.1928	-0.0486	-0.2515	0.0417	0.0313	0.0097	0.0281	0.098	-0.0321	0.0486	-19.1255	-13.6825	39.3173
11	0.0555	0.2758	0.3858	1.8441	0.8431	5.5519	-0.0381	-0.0625	0.047	-0.1445	-0.1908	0.3161	-0.1416	-0.7246	0.2288	0.0588	0.0178	-0.0063	0.1842	-0.0476	0.1059	-27.2317	-18.6207	22.9135
12	1.6845	1.1431	0.1162	3.611	0.6109	0.8747	-0.0466	0	0.2482	-0.0038	-0.0072	0.3121	-0.1543	-0.212	0.0538	0.0461	0.0545	-0.0044	0.0793	-0.0197	0.0799	-19.5758	-6.0147	23.3957
13	0.4958	0.6415	0.0718	1.7802	0.1	0.3377	0.0048	-0.0128	0.0133	-0.0078	-0.0002	0.0605	-0.008	-0.0778	-0.0046	0.0259	0.0027	-0.0026	0.0597	0.0097	0.0718	-15.7729	-22.0445	17.4658
14	0.7922	0.4036	0.6686	0.5402	0.2748	0.8923	-0.0255	-0.0847	0.1163	0.0565	-0.0464	0.0593	-0.0199	-0.0072	0.0719	0.0509	0.0155	-0.0003	0.0584	-0.0123	0.0651	-4.1819	-13.165	28.0005
15	0.5205	0.0344	0.0694	0.4961	0.0907	0.3136	0.0053	-0.1546	0.0135	0.1412	-0.0401	0.0599	0.006	-0.1143	0.0348	0.0687	-0.013	0.0285	0.0846	-0.0194	0.0305	-13.9464	-19.1775	40.0751
16	4.5379	-1.2919	1.1328	2.148	-2.1108	6.4897	-0.0933	-0.018	0.2639	0.1704	-0.0091	0.1314	-0.6778	-0.0322	0.1024	0.2157	-0.003	-0.0436	0.014	-0.0372	0.1439	-7.8689	6.2495	30.6444
17	0.6709	-0.0636	-0.1117	0.3688	0.2046	0.6838	-0.0221	-0.1554	0.072	0.1586	0.0034	-0.0005	-0.0297	-0.0173	0.0187	0.0968	-0.0033	-0.0023	0.07	-0.0282	0.0236	-3.7925	-13.0528	45.4387
18	0.8108	0.3347	-0.2426	0.9926	0.1892	1.0488	0.0323	-0.1884	0.149	0.1703	-0.0257	0.0687	-0.0865	-0.0026	-0.0067	0.0967	0.0007	0.0009	0.0723	-0.0487	0.038	-7.1916	-9.2865	49.1338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 63
2	X-RAY DIFFRACTION	2	A	64 - 82
3	X-RAY DIFFRACTION	3	A	83 - 102
4	X-RAY DIFFRACTION	4	A	103 - 160
5	X-RAY DIFFRACTION	5	A	161 - 183
6	X-RAY DIFFRACTION	6	A	184 - 251
7	X-RAY DIFFRACTION	7	A	252 - 266
8	X-RAY DIFFRACTION	8	A	267 - 372
9	X-RAY DIFFRACTION	9	A	373 - 416
10	X-RAY DIFFRACTION	10	B	4 - 63
11	X-RAY DIFFRACTION	11	B	64 - 82
12	X-RAY DIFFRACTION	12	B	83 - 102
13	X-RAY DIFFRACTION	13	B	103 - 160
14	X-RAY DIFFRACTION	14	B	161 - 183
15	X-RAY DIFFRACTION	15	B	184 - 251
16	X-RAY DIFFRACTION	16	B	252 - 266
17	X-RAY DIFFRACTION	17	B	267 - 372
18	X-RAY DIFFRACTION	18	B	373 - 416

-
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, 2 molecules AB

-
Non-polymers , 6 types, 768 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, 2 molecules AB

-Non-polymers , 6 types, 768 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, 2 molecules AB

-
Non-polymers , 6 types, 768 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