PDB-6ito: Crystal structure of pyruvate kinase (PYK) from Mycobacterium tub...

ID or keywords:

Entry

Database: PDB / ID: 6ito

Title

Crystal structure of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, AMP and inhibitor Ribose 5-Phosphate

Components

Pyruvate kinase

Keywords

TRANSFERASE /

pyruvate kinase /

glycolysis /

tetramer /

allostery /

synergism / phospho transferase

Function / homology

Function and homology information

pyruvate kinase /

pyruvate kinase activity /

potassium ion binding / glycolytic process /

kinase activity /

phosphorylation / magnesium ion binding /

ATP binding /

plasma membrane /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Zhong, W. / Cai, Q. / El Sahili, A. / Mu, Y. / Lescar, J. / Dedon, P.C.

Funding support

Singapore, 1items

Citation

Journal: J.Mol.Biol. / Year: 2019
Title: Pyruvate Kinase Regulates the Pentose-Phosphate Pathway in Response to Hypoxia in Mycobacterium tuberculosis.
Authors: Zhong, W. / Guo, J. / Cui, L. / Chionh, Y.H. / Li, K. / El Sahili, A. / Cai, Q. / Yuan, M. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. / Mu, Y. / Lescar, J. / Dedon, P.C.

History

Deposition	Nov 24, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 14, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Sep 25, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Nov 22, 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_ncs_dom_lim 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_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.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.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_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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ito.cif.gz	727.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/it/6ito ftp://data.pdbj.org/pub/pdb/validation_reports/it/6ito	HTTPS FTP

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Related structure data

Related structure data	5wscS S: Starting model for refinement
Similar structure data	5wsb-d 5wsa-d 5wsc-d 5ws9-d 5ws8-d 6qxl-3 6qxl-1 4l28-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (13) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Pyruvate kinase

B: Pyruvate kinase

C: Pyruvate kinase

D: Pyruvate kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	125.550, 125.550, 143.821
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 2 - 472 / Label seq-ID: 5 - 475

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	B	B
2	4	C	C
1	5	B	B
2	5	D	D
1	6	C	C
2	6	D	D

NCS ensembles :

ID
1
2
3
4
5
6

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein	Pyruvate kinase / / PK Mass: 51014.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Plasmid: pYUB28b-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5, pyruvate kinase
#4: Sugar	ChemComp-R5P / RIBOSE-5-PHOSPHATE / Ribose 5-phosphate Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₅H₁₁O₈P

#1: Protein

Pyruvate kinase /

/ PK

Mass: 51014.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Plasmid: pYUB28b-TEV / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5,

pyruvate kinase

#4: Sugar

ChemComp-R5P / RIBOSE-5-PHOSPHATE /

Ribose 5-phosphate

Type: saccharide

Carbohydrate / Mass: 230.110 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₅H₁₁O₈P

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Non-polymers , 4 types, 552 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-OXL / OXALATE ION / Oxalate Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂O₄
#5: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.23 Å³/Da / Density % sol: 61.91 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM AMP, 5 mM D-ribose 5-phosphate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 3, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.55→62.77 Å / Num. obs: 82657 / % possible obs: 100 % / Redundancy: 4 % / B_iso Wilson estimate: 38.9 Å² / R_merge(I) obs: 0.124 / Net I/σ(I): 8.8
Reflection shell	Resolution: 2.55→2.6 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.94 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4510 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0232	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5WSC

5wsc

Resolution: 2.55→62.77 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.92 / SU B: 30.649 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.28 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24762	4106	5 %	RANDOM
R_work	0.20567	-	-	-
obs	0.20773	78503	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 54.418 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.36 Å²	0.68 Å²	0 Å²
2-	-	1.36 Å²	0 Å²
3-	-	-	-4.4 Å²

Refinement step

Cycle: 1 / Resolution: 2.55→62.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14172	0	176	540	14888

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	14580
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	14095
X-RAY DIFFRACTION	r_angle_refined_deg	1.219	1.655	19823
X-RAY DIFFRACTION	r_angle_other_deg	1.16	1.585	32479
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.185	5	1886
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.22	20.509	746
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.41	15	2457
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.377	15	151
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1979
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	16388
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2965
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	1.574	3.082	7547
X-RAY DIFFRACTION	r_mcbond_other	1.573	3.082	7546
X-RAY DIFFRACTION	r_mcangle_it	2.589	4.621	9432
X-RAY DIFFRACTION	r_mcangle_other	2.59	4.622	9433
X-RAY DIFFRACTION	r_scbond_it	1.64	3.324	7033
X-RAY DIFFRACTION	r_scbond_other	1.64	3.323	7031
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.677	4.922	10391
X-RAY DIFFRACTION	r_long_range_B_refined	5.633	59.156	60613
X-RAY DIFFRACTION	r_long_range_B_other	5.632	59.156	60614
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	14626	0.07
1	2	B	14626	0.07
2	1	A	14608	0.07
2	2	C	14608	0.07
3	1	A	14652	0.07
3	2	D	14652	0.07
4	1	B	14681	0.05
4	2	C	14681	0.05
5	1	B	14691	0.06
5	2	D	14691	0.06
6	1	C	14659	0.06
6	2	D	14659	0.06

LS refinement shell

Resolution: 2.55→2.617 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.34	297	-
R_work	0.36	5898	-
obs	-	-	99.92 %

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	2.7915	-1.3957	0.8615	5.2364	0.1618	1.9806	-0.3183	-0.2619	0.1531	0.0978	0.2262	-0.5841	-0.2375	0.4506	0.0921	0.2171	0.1595	-0.036	0.4986	-0.0249	0.0767	-24.7046	-2.886	29.8849
2	2.6891	-0.0686	1.0578	3.2428	-2.4343	6.6124	0.0312	0.2592	-0.2046	-0.1672	-0.0421	-0.2506	0.2923	0.7246	0.0108	0.3878	0.0207	0.0197	0.5051	-0.0313	0.3091	-14.0536	-24.8176	7.7415
3	2.0414	-0.2099	0.2212	1.5187	-0.3022	2.3837	-0.2739	-0.1402	-0.2087	0.0787	0.194	-0.0327	0.1301	0.0001	0.0799	0.1164	0.1057	0.0296	0.3264	-0.0252	0.0319	-33.0957	-9.7761	18.7378
4	5.0238	-0.2965	0.2328	1.1001	-0.5269	2.4834	-0.1238	-0.3385	0.1582	0.1924	0.0783	0.0336	-0.0504	0.0231	0.0456	0.1743	0.1745	-0.0052	0.399	-0.047	0.0391	-51.0838	0.9164	34.1109
5	2.7901	1.7787	-0.6364	5.813	-0.5592	1.4777	-0.3185	0.2659	-0.2404	-0.1453	0.2231	-0.6283	0.1758	0.4653	0.0953	0.2239	-0.1671	0.0365	0.5009	-0.0415	0.0715	-24.6919	2.9008	-18.4909
6	2.6309	-0.6207	-1.5763	2.5658	-3.1112	6.2804	0.0486	-0.2779	0.1336	0.1483	-0.1108	-0.1437	-0.361	0.8088	0.0622	0.4136	-0.0297	-0.0295	0.5437	-0.0488	0.3352	-14.0602	24.7824	3.6454
7	1.8534	0.2991	-0.3876	1.8676	-0.5286	2.3349	-0.2906	0.1605	0.2149	-0.0399	0.176	-0.0385	-0.1598	0.0124	0.1146	0.1216	-0.1198	-0.0384	0.3242	-0.0228	0.0429	-33.1008	9.7906	-7.3465
8	5.1893	0.2011	0.0324	1.2533	-0.5587	3.1651	-0.102	0.3889	-0.155	-0.1901	0.0379	0.0551	0.0342	-0.0042	0.0642	0.1778	-0.1762	0.0209	0.3751	-0.0438	0.0174	-51.0911	-0.9151	-22.6874
9	2.6688	-1.4208	-0.7212	5.314	-0.0392	2.138	-0.3301	-0.2776	-0.1944	0.1535	0.2105	0.6773	0.197	-0.4481	0.1197	0.1954	0.1684	0.0468	0.495	0.0345	0.0987	-100.8384	2.8963	29.89
10	2.2278	0.3088	-1.5831	2.6931	2.7612	6.5028	0.0302	0.2646	0.1076	-0.1623	-0.0595	0.1326	-0.3344	-0.8371	0.0293	0.4028	0.035	-0.0211	0.5451	0.0546	0.3277	-111.4848	24.7672	7.7504
11	1.955	-0.1802	-0.1518	1.8161	0.5194	2.442	-0.2855	-0.1216	0.2369	0.0696	0.1706	0.0254	-0.1833	-0.0602	0.1149	0.1189	0.123	-0.0323	0.3371	0.0304	0.0434	-92.4325	9.7878	18.7467
12	5.0638	-0.4812	0.0856	1.2921	0.4937	3.3189	-0.1055	-0.3386	-0.1553	0.2004	0.0507	-0.0316	0.0296	-0.0327	0.0548	0.1608	0.167	0.0188	0.384	0.0387	0.0303	-74.4344	-0.9005	34.0779
13	3.0662	1.241	0.4644	5.0864	-0.0387	1.4628	-0.3542	0.2198	0.2135	-0.2034	0.2157	0.5746	-0.1614	-0.5122	0.1385	0.2232	-0.1799	-0.061	0.5089	0.01	0.0828	-100.842	-2.8993	-18.4817
14	2.2573	-0.4896	0.9841	3.2303	2.3692	6.6388	0.0162	-0.2165	-0.1948	0.0971	-0.0729	0.2447	0.3923	-0.8957	0.0566	0.3846	-0.0349	-0.0029	0.5506	0.0481	0.3125	-111.5229	-24.7705	3.6759
15	1.7597	0.2635	0.2875	1.6175	0.2899	2.3851	-0.2783	0.1501	-0.2256	-0.0734	0.2031	0.023	0.1409	-0.0384	0.0752	0.1179	-0.1097	0.0353	0.3332	0.0226	0.0409	-92.4276	-9.7839	-7.3354
16	5.1329	0.0612	0.0315	1.2044	0.6391	2.7411	-0.114	0.348	0.1416	-0.1719	0.0477	-0.0591	-0.0696	-0.0165	0.0663	0.1686	-0.1753	-0.0098	0.3873	0.0456	0.0268	-74.4476	0.919	-22.6781

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 70
2	X-RAY DIFFRACTION	2	A	71 - 167
3	X-RAY DIFFRACTION	3	A	168 - 344
4	X-RAY DIFFRACTION	4	A	345 - 467
5	X-RAY DIFFRACTION	5	B	2 - 70
6	X-RAY DIFFRACTION	6	B	71 - 167
7	X-RAY DIFFRACTION	7	B	168 - 344
8	X-RAY DIFFRACTION	8	B	345 - 467
9	X-RAY DIFFRACTION	9	C	2 - 70
10	X-RAY DIFFRACTION	10	C	71 - 167
11	X-RAY DIFFRACTION	11	C	168 - 344
12	X-RAY DIFFRACTION	12	C	345 - 467
13	X-RAY DIFFRACTION	13	D	2 - 70
14	X-RAY DIFFRACTION	14	D	71 - 167
15	X-RAY DIFFRACTION	15	D	168 - 344
16	X-RAY DIFFRACTION	16	D	345 - 467

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Protein / Sugars , 2 types, 8 molecules ABCD

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Non-polymers , 4 types, 552 molecules

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-Protein / Sugars , 2 types, 8 molecules ABCD

-Non-polymers , 4 types, 552 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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

-Aug 12, 2020. Covid-19 info

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

-
Non-polymers , 4 types, 552 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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

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Jul 12, 2017. Major update of PDB

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Yorodumi