PDB-7od0: Mirolysin in complex with compound 9

ID or keywords:

Entry

Database: PDB / ID: 7od0

Title

Mirolysin in complex with compound 9

Components

Mirolysin

Keywords

HYDROLASE / Bacterial protease

Function / homology

Function and homology information

metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function

Biological species

Tannerella forsythia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Zak, K.M. / Bostock, M.J. / Ksiazek, M.

Funding support

Poland, 2items

Citation

Journal: J Enzyme Inhib Med Chem / Year: 2021
Title: Latency, thermal stability, and identification of an inhibitory compound of mirolysin, a secretory protease of the human periodontopathogen Tannerella forsythia .
Authors: Zak, K.M. / Bostock, M.J. / Waligorska, I. / Thogersen, I.B. / Enghild, J.J. / Popowicz, G.M. / Grudnik, P. / Potempa, J. / Ksiazek, M.

History

Deposition	Apr 28, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 4, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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Download

PDBx/mmCIF format	7od0.cif.gz	648.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7od0.ent.gz		Display	PDB format
PDBx/mmJSON format	7od0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7od0_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	7od0_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7od0_validation.xml.gz	73.2 KB	Display
Data in CIF	7od0_validation.cif.gz	101.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/od/7od0 ftp://data.pdbj.org/pub/pdb/validation_reports/od/7od0	HTTPS FTP

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Related structure data

Related structure data	6r7wS S: Starting model for refinement
Similar structure data	7od0-3 6v1j-d 4n15-d 5ul8-d 1woq-1 5q0r-d 6aqk-d 4uaa-2 4n17-d 6i99-2 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) 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

6r7wS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#28 - Apr 2002 Anthrax Toxin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

AAA: Mirolysin

BBB: Mirolysin

CCC: Mirolysin

DDD: Mirolysin

EEE: Mirolysin

FFF: Mirolysin

hetero molecules

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

1

AAA: Mirolysin

hetero molecules

defined by author
Evidence: gel filtration
31.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Mirolysin

hetero molecules

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

3

CCC: Mirolysin

hetero molecules

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

4

DDD: Mirolysin

hetero molecules

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

5

EEE: Mirolysin

hetero molecules

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

6

FFF: Mirolysin

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.593, 77.640, 81.995
Angle α, β, γ (deg.)	92.462, 90.000, 119.980
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

End auth comp-ID: PRO / End label comp-ID: PRO

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	AAA	A	59 - 327	5 - 273
2	1	1	SER	SER	BBB	B	59 - 327	5 - 273
3	2	2	SER	SER	AAA	A	59 - 327	5 - 273
4	2	2	SER	SER	CCC	C	59 - 327	5 - 273
5	3	3	SER	SER	AAA	A	59 - 327	5 - 273
6	3	3	SER	SER	DDD	D	59 - 327	5 - 273
7	4	4	SER	SER	AAA	A	59 - 327	5 - 273
8	4	4	SER	SER	EEE	E	59 - 327	5 - 273
9	5	5	SER	SER	AAA	A	59 - 327	5 - 273
10	5	5	SER	SER	FFF	F	59 - 327	5 - 273
11	6	6	PRO	PRO	BBB	B	58 - 327	4 - 273
12	6	6	PRO	PRO	CCC	C	58 - 327	4 - 273
13	7	7	PRO	PRO	BBB	B	58 - 327	4 - 273
14	7	7	PRO	PRO	DDD	D	58 - 327	4 - 273
15	8	8	PRO	PRO	BBB	B	58 - 327	4 - 273
16	8	8	PRO	PRO	EEE	E	58 - 327	4 - 273
17	9	9	PRO	PRO	BBB	B	58 - 327	4 - 273
18	9	9	PRO	PRO	FFF	F	58 - 327	4 - 273
19	10	10	PRO	PRO	CCC	C	58 - 327	4 - 273
20	10	10	PRO	PRO	DDD	D	58 - 327	4 - 273
21	11	11	PRO	PRO	CCC	C	58 - 327	4 - 273
22	11	11	PRO	PRO	EEE	E	58 - 327	4 - 273
23	12	12	PRO	PRO	CCC	C	58 - 327	4 - 273
24	12	12	PRO	PRO	FFF	F	58 - 327	4 - 273
25	13	13	PRO	PRO	DDD	D	58 - 327	4 - 273
26	13	13	PRO	PRO	EEE	E	58 - 327	4 - 273
27	14	14	PRO	PRO	DDD	D	58 - 327	4 - 273
28	14	14	PRO	PRO	FFF	F	58 - 327	4 - 273
29	15	15	PRO	PRO	EEE	E	58 - 327	4 - 273
30	15	15	PRO	PRO	FFF	F	58 - 327	4 - 273

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

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Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

#1: Protein	Mirolysin Mass: 30987.145 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7IPS1

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Non-polymers , 7 types, 1109 molecules

#2: Chemical	ChemComp-V7Q / 2,1,3-benzothiadiazol-4-ylmethanamine / Benzo[c][1,2,5]thiadiazol-4-ylmethanamine / 2795209 Mass: 165.216 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₇H₇N₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1067 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.49 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M Zinc acetate dihydrate, 0.1 M Sodium acetate pH 4.5, 10% (v/v) PEG 3000

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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: Feb 18, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.1→40.95 Å / Num. obs: 88998 / % possible obs: 92.2 % / Redundancy: 2.6 % / CC_1/2: 0.983 / R_merge(I) obs: 0.097 / R_pim(I) all: 0.097 / R_rim(I) all: 0.137 / Net I/σ(I): 7.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8-10	2.7	0.061	601	0.99	0.061	0.086
2.1-2.14	2.5	0.24	4272	0.93	0.24	0.339

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Aimless	0.7.4	data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6r7w

6r7w

Resolution: 2.1→38.803 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.896 / WR_factor R_free: 0.242 / WR_factor R_work: 0.213 / SU B: 5.696 / SU ML: 0.148 / Average fsc free: 0.9038 / Average fsc work: 0.9118 / Cross valid method: FREE R-VALUE / ESU R: 0.319 / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2304	4127	4.637 %
R_work	0.2038	84871	-
all	0.205	-	-
obs	-	88998	92.155 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 15.477 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.772 Å²	-0.437 Å²	-0.287 Å²
2-	-	-1.891 Å²	0.341 Å²
3-	-	-	5.351 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→38.803 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12659	0	147	1067	13873

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	13529
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	12106
X-RAY DIFFRACTION	r_angle_refined_deg	1.455	1.649	18465
X-RAY DIFFRACTION	r_angle_other_deg	1.312	1.582	27876
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.072	5	1764
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.899	23.147	788
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.748	15	2177
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	8.99	15	17
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.971	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1797
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	17640
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3396
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	2944
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	12224
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	6663
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	6170
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.204	0.2	885
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.137	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.122	0.2	52
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.399	0.2	86
X-RAY DIFFRACTION	r_nbd_other	0.248	0.2	351
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.324	0.2	44
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.301	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.372	1.519	6631
X-RAY DIFFRACTION	r_mcbond_other	1.369	1.518	6629
X-RAY DIFFRACTION	r_mcangle_it	2.356	2.265	8313
X-RAY DIFFRACTION	r_mcangle_other	2.356	2.266	8314
X-RAY DIFFRACTION	r_scbond_it	1.539	1.661	6898
X-RAY DIFFRACTION	r_scbond_other	1.538	1.661	6899
X-RAY DIFFRACTION	r_scangle_it	2.562	2.437	10079
X-RAY DIFFRACTION	r_scangle_other	2.561	2.437	10080
X-RAY DIFFRACTION	r_lrange_it	5.296	28.224	60039
X-RAY DIFFRACTION	r_lrange_other	5.189	28.035	59438
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.054	0.05	9441
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.062	0.05	9360
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.066	0.05	9409
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.059	0.05	9417
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.061	0.05	9399
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.058	0.05	9388
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.064	0.05	9431
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.059	0.05	9444
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.058	0.05	9406
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.058	0.05	9406
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.061	0.05	9292
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.048	0.05	9368
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.061	0.05	9418
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.056	0.05	9470
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.058	0.05	9312

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.05448	0.05011
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.05448	0.05011
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.06225	0.0501
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.06225	0.0501
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.06581	0.05011
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.06581	0.05011
4	7	AAA	X-RAY DIFFRACTION	Local ncs	0.05945	0.05011
4	8	EEE	X-RAY DIFFRACTION	Local ncs	0.05945	0.05011
5	9	AAA	X-RAY DIFFRACTION	Local ncs	0.06067	0.05011
5	10	FFF	X-RAY DIFFRACTION	Local ncs	0.06067	0.05011
6	11	BBB	X-RAY DIFFRACTION	Local ncs	0.05763	0.05011
6	12	CCC	X-RAY DIFFRACTION	Local ncs	0.05763	0.05011
7	13	BBB	X-RAY DIFFRACTION	Local ncs	0.0636	0.05011
7	14	DDD	X-RAY DIFFRACTION	Local ncs	0.0636	0.05011
8	15	BBB	X-RAY DIFFRACTION	Local ncs	0.05867	0.05011
8	16	EEE	X-RAY DIFFRACTION	Local ncs	0.05867	0.05011
9	17	BBB	X-RAY DIFFRACTION	Local ncs	0.05771	0.05011
9	18	FFF	X-RAY DIFFRACTION	Local ncs	0.05771	0.05011
10	19	CCC	X-RAY DIFFRACTION	Local ncs	0.05843	0.0501
10	20	DDD	X-RAY DIFFRACTION	Local ncs	0.05843	0.0501
11	21	CCC	X-RAY DIFFRACTION	Local ncs	0.06094	0.0501
11	22	EEE	X-RAY DIFFRACTION	Local ncs	0.06094	0.0501
12	23	CCC	X-RAY DIFFRACTION	Local ncs	0.04846	0.05011
12	24	FFF	X-RAY DIFFRACTION	Local ncs	0.04846	0.05011
13	25	DDD	X-RAY DIFFRACTION	Local ncs	0.06131	0.05011
13	26	EEE	X-RAY DIFFRACTION	Local ncs	0.06131	0.05011
14	27	DDD	X-RAY DIFFRACTION	Local ncs	0.05551	0.05011
14	28	FFF	X-RAY DIFFRACTION	Local ncs	0.05551	0.05011
15	29	EEE	X-RAY DIFFRACTION	Local ncs	0.05761	0.05011
15	30	FFF	X-RAY DIFFRACTION	Local ncs	0.05761	0.05011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.1-2.154	0.303	280	0.248	5869	0.25	7118	0.756	0.804	86.3866	0.23
2.154-2.213	0.259	207	0.229	5860	0.23	6951	0.843	0.855	87.2824	0.213
2.213-2.277	0.247	200	0.216	5647	0.217	6732	0.867	0.871	86.8538	0.202
2.277-2.347	0.254	211	0.206	5563	0.208	6563	0.871	0.897	87.9781	0.193
2.347-2.424	0.226	292	0.203	5316	0.204	6353	0.9	0.906	88.2733	0.193
2.424-2.508	0.229	243	0.196	5278	0.198	6197	0.916	0.925	89.0915	0.187
2.508-2.603	0.22	234	0.187	5069	0.188	5849	0.924	0.933	90.6651	0.18
2.603-2.708	0.241	228	0.185	5020	0.187	5736	0.924	0.934	91.4923	0.18
2.708-2.828	0.214	253	0.186	4830	0.187	5528	0.929	0.934	91.9501	0.182
2.828-2.966	0.229	278	0.193	4573	0.195	5233	0.919	0.927	92.7002	0.194
2.966-3.125	0.208	261	0.185	4502	0.186	5036	0.933	0.939	94.579	0.193
3.125-3.313	0.224	254	0.205	4246	0.206	4676	0.929	0.931	96.2361	0.214
3.313-3.54	0.236	245	0.201	4123	0.203	4478	0.926	0.932	97.5435	0.213
3.54-3.821	0.215	183	0.194	3828	0.195	4063	0.937	0.944	98.7202	0.213
3.821-4.182	0.199	239	0.187	3536	0.188	3821	0.949	0.956	98.7961	0.207
4.182-4.668	0.187	125	0.176	3280	0.176	3442	0.95	0.957	98.925	0.198
4.668-5.378	0.229	146	0.197	2859	0.199	3040	0.942	0.948	98.8487	0.233
5.378-6.555	0.277	113	0.252	2435	0.253	2562	0.883	0.911	99.4536	0.289
6.555-9.141	0.225	82	0.25	1926	0.249	2018	0.922	0.925	99.5045	0.287
9.141-38.803	0.439	53	0.371	1111	0.374	1167	0.895	0.914	99.7429	0.447

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Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

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Non-polymers , 7 types, 1109 molecules

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-Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

-Non-polymers , 7 types, 1109 molecules

-Details

-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

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+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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Open data

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Validation report

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Related structure data

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Assembly

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Components

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Protein , 1 types, 6 molecules AAABBBCCCDDDEEEFFF

-
Non-polymers , 7 types, 1109 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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

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Yorodumi