PDB-3m9b: Crystal structure of the amino terminal coiled coil domain and th...

ID or keywords:

Entry

Database: PDB / ID: 3m9b

Title

Crystal structure of the amino terminal coiled coil domain and the inter domain of the Mycobacterium tuberculosis proteasomal ATPase Mpa

Components

Proteasome-associated ATPase

Keywords

CHAPERONE / coil coil with 5 beta-strand barrel inter domain

Function / homology

Function and homology information

ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / cell wall / retrograde protein transport, ER to cytosol / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / protein unfolding ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.94 Å

Authors

Li, H. / Wang, T.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation.
Authors: Wang, T. / Darwin, K.H. / Li, H.

History

Deposition	Mar 21, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3m9b.cif.gz	888.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3m9b.ent.gz	749.8 KB	Display	PDB format
PDBx/mmJSON format	3m9b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3m9b_validation.pdf.gz	573 KB	Display	wwPDB validaton report
Full document	3m9b_full_validation.pdf.gz	701.8 KB	Display
Data in XML	3m9b_validation.xml.gz	91 KB	Display
Data in CIF	3m9b_validation.cif.gz	119.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/3m9b ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m9b	HTTPS FTP

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Related structure data

Related structure data	3m91C 3m9dC 3m9hC C: citing same article (ref.)
Similar structure data	3m9d-1 3m9d-2 8631 22301 7dnk-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) 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	#32 - Aug 2002 Chaperones similarity (1) #166 - Oct 2013 Proteasome similarity (4) #80 - Aug 2006 AAA+ Proteases similarity (2) #167 - Nov 2013 SNARE Proteins similarity (2)

Deposited unit

A: Proteasome-associated ATPase

B: Proteasome-associated ATPase

C: Proteasome-associated ATPase

D: Proteasome-associated ATPase

E: Proteasome-associated ATPase

F: Proteasome-associated ATPase

G: Proteasome-associated ATPase

H: Proteasome-associated ATPase

I: Proteasome-associated ATPase

J: Proteasome-associated ATPase

K: Proteasome-associated ATPase

L: Proteasome-associated ATPase

330 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Proteasome-associated ATPase

B: Proteasome-associated ATPase

C: Proteasome-associated ATPase

D: Proteasome-associated ATPase

E: Proteasome-associated ATPase

F: Proteasome-associated ATPase

defined by author&software
165 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: Proteasome-associated ATPase

H: Proteasome-associated ATPase

I: Proteasome-associated ATPase

J: Proteasome-associated ATPase

K: Proteasome-associated ATPase

L: Proteasome-associated ATPase

defined by author&software
165 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	176.787, 176.652, 176.633
Angle α, β, γ (deg.)	90.000, 90.040, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 2

Dom-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	PRO	PRO	A	A	98 - 237	98 - 237
2	1	PRO	PRO	B	B	98 - 237	98 - 237
3	1	PRO	PRO	C	C	98 - 237	98 - 237
4	1	PRO	PRO	D	D	98 - 237	98 - 237
5	1	PRO	PRO	E	E	98 - 237	98 - 237
6	1	PRO	PRO	F	F	98 - 237	98 - 237
1	2	SER	SER	A	A	52 - 97	52 - 97
2	2	SER	SER	C	C	52 - 97	52 - 97
3	2	SER	SER	E	E	52 - 97	52 - 97
1	3	SER	SER	B	B	52 - 97	52 - 97
2	3	SER	SER	D	D	52 - 97	52 - 97
3	3	SER	SER	F	F	52 - 97	52 - 97
1	4	PRO	PRO	G	G	98 - 237	98 - 237
2	4	PRO	PRO	H	H	98 - 237	98 - 237
3	4	PRO	PRO	I	I	98 - 237	98 - 237
4	4	PRO	PRO	J	J	98 - 237	98 - 237
5	4	PRO	PRO	K	K	98 - 237	98 - 237
6	4	PRO	PRO	L	L	98 - 237	98 - 237
1	5	SER	SER	G	G	52 - 97	52 - 97
2	5	SER	SER	I	I	52 - 97	52 - 97
3	5	SER	SER	K	K	52 - 97	52 - 97
1	6	SER	SER	H	H	52 - 97	52 - 97
2	6	SER	SER	J	J	52 - 97	52 - 97
3	6	SER	SER	L	L	52 - 97	52 - 97

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / ARC / Mycobacterial proteasome ATPase Mass: 27491.785 Da / Num. of mol.: 12 / Fragment: Coil Coil inter domain (UNP residues: 1-234) Source method: isolated from a genetically manipulated source Details: IPTG inducible expression / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: mpa / Plasmid: pET24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P63345, UniProt: P9WQN5*PLUS

#1: Protein

Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / ARC / Mycobacterial proteasome ATPase

Mass: 27491.785 Da / Num. of mol.: 12 / Fragment: Coil Coil inter domain (UNP residues: 1-234)
Source method: isolated from a genetically manipulated source
Details: IPTG inducible expression / Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: mpa / Plasmid: pET24b(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P63345, UniProt: P9WQN5*PLUS

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 8.4 Å³/Da / Density % sol: 85.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30%v/v Tacsimate (1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, 0.16 M Ammonium ...Details: 30%v/v Tacsimate (1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, 0.16 M Ammonium tartrate dibasic), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 8.4 Å³/Da / Density % sol: 85.3 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30%v/v Tacsimate (1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, 0.16 M Ammonium ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2009
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0809 Å / Relative weight: 1
Reflection	Resolution: 3.94→25 Å / Num. all: 104826 / Num. obs: 98265 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / R_merge(I) obs: 0.046 / R_sym value: 0.066
Reflection shell	Resolution: 3.94→4.01 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.51 / R_sym value: 0.65 / % possible all: 60

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX		model building
REFMAC	5.5.0109	refinement
DENZO		data reduction
SCALEPACK		data scaling
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 3.94→25 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.894 / SU B: 70.518 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R: 0.701 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30369	5010	5.1 %	RANDOM
R_work	0.27472	-	-	-
obs	0.2762	93255	99.68 %	-

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: 239.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0 Å²	-0 Å²	-0 Å²
2-	-	-0 Å²	0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: LAST / Resolution: 3.94→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17172	0	0	0	17172

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	17424
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.234	1.995	23652
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.305	5	2220
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.164	23.731	804
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	25.017	15	3048
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.727	15	192
X-RAY DIFFRACTION	r_chiral_restr	0.15	0.2	2784
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	13188
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	560	TIGHT POSITIONAL	0.49	0.05
1	2	B	560	TIGHT POSITIONAL	0.48	0.05
1	3	C	560	TIGHT POSITIONAL	0.5	0.05
1	4	D	560	TIGHT POSITIONAL	0.48	0.05
1	5	E	560	TIGHT POSITIONAL	0.48	0.05
1	6	F	560	TIGHT POSITIONAL	0.47	0.05
1	1	A	504	MEDIUM POSITIONAL	0.83	0.5
1	2	B	504	MEDIUM POSITIONAL	0.81	0.5
1	3	C	504	MEDIUM POSITIONAL	0.84	0.5
1	4	D	504	MEDIUM POSITIONAL	0.85	0.5
1	5	E	504	MEDIUM POSITIONAL	0.84	0.5
1	6	F	504	MEDIUM POSITIONAL	0.84	0.5
2	1	A	184	TIGHT POSITIONAL	0.01	0.05
2	2	C	184	TIGHT POSITIONAL	0.01	0.05
2	3	E	184	TIGHT POSITIONAL	0.01	0.05
2	1	A	184	MEDIUM POSITIONAL	0.02	0.5
2	2	C	184	MEDIUM POSITIONAL	0.02	0.5
2	3	E	184	MEDIUM POSITIONAL	0.02	0.5
3	1	B	184	TIGHT POSITIONAL	0.01	0.05
3	2	D	184	TIGHT POSITIONAL	0.01	0.05
3	3	F	184	TIGHT POSITIONAL	0.01	0.05
3	1	B	184	MEDIUM POSITIONAL	0.01	0.5
3	2	D	184	MEDIUM POSITIONAL	0.01	0.5
3	3	F	184	MEDIUM POSITIONAL	0.02	0.5
4	1	G	560	TIGHT POSITIONAL	0.5	0.05
4	2	H	560	TIGHT POSITIONAL	0.49	0.05
4	3	I	560	TIGHT POSITIONAL	0.48	0.05
4	4	J	560	TIGHT POSITIONAL	0.49	0.05
4	5	K	560	TIGHT POSITIONAL	0.49	0.05
4	6	L	560	TIGHT POSITIONAL	0.48	0.05
4	1	G	504	MEDIUM POSITIONAL	0.84	0.5
4	2	H	504	MEDIUM POSITIONAL	0.84	0.5
4	3	I	504	MEDIUM POSITIONAL	0.83	0.5
4	4	J	504	MEDIUM POSITIONAL	0.84	0.5
4	5	K	504	MEDIUM POSITIONAL	0.83	0.5
4	6	L	504	MEDIUM POSITIONAL	0.82	0.5
5	1	G	184	TIGHT POSITIONAL	0.01	0.05
5	2	I	184	TIGHT POSITIONAL	0.01	0.05
5	3	K	184	TIGHT POSITIONAL	0.01	0.05
5	1	G	184	MEDIUM POSITIONAL	0.02	0.5
5	2	I	184	MEDIUM POSITIONAL	0.02	0.5
5	3	K	184	MEDIUM POSITIONAL	0.02	0.5
6	1	H	184	TIGHT POSITIONAL	0.01	0.05
6	2	J	184	TIGHT POSITIONAL	0.01	0.05
6	3	L	184	TIGHT POSITIONAL	0.01	0.05
6	1	H	184	MEDIUM POSITIONAL	0.01	0.5
6	2	J	184	MEDIUM POSITIONAL	0.01	0.5
6	3	L	184	MEDIUM POSITIONAL	0.01	0.5

LS refinement shell

Resolution: 3.9→3.999 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.41	354	-
R_work	0.387	6679	-
all	-	7033	-
obs	-	-	99.65 %

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	0.5058	-0.2723	1.1228	0.9217	-2.0067	5.076	-0.2496	0.0251	0.3893	0.0842	-0.0442	0.1074	-0.5598	-0.0757	0.2937	0.5291	0.3557	-0.2994	0.3074	-0.0813	0.4643	-38.1984	41.9494	-25.8152
2	1.1473	1.2942	-1.0399	5.3279	-5.1109	5.0184	-0.1335	0.3137	0.0659	-0.376	0.1796	0.2459	0.1832	-0.1938	-0.046	0.4024	0.2679	-0.3558	0.488	-0.2639	0.3232	-41.2914	31.9874	-40.8255
3	1.11	2.2672	0.3147	5.0802	1.0428	0.4794	-0.0133	-0.0913	-0.0586	0.0989	0.2203	-0.4209	-0.0434	0.3636	-0.2069	0.343	0.06	-0.3822	0.4319	-0.2857	0.547	-1.7642	25.3795	-6.0009
4	5.2099	5.1805	-1.4685	5.2783	-1.233	1.32	0.219	-0.2546	0.4069	0.2351	-0.0579	0.227	-0.3392	0.1081	-0.1611	0.4883	0.2459	-0.2925	0.2944	-0.3307	0.3918	-11.7397	40.3661	-2.8721
5	5.0429	-1.2336	-2.1971	0.554	0.3683	1.0861	0.2806	0.4718	-0.0124	-0.3704	-0.2206	-0.021	0.1039	-0.0637	-0.06	0.4391	0.3068	-0.1131	0.5055	-0.3421	0.2869	-18.3178	5.5391	-42.3946
6	5.144	1.0175	-4.9851	1.1019	-1.2779	5.0144	-0.0425	-0.2031	-0.1679	-0.1023	-0.1195	-0.3134	0.2943	0.4107	0.162	0.3386	0.3444	-0.2667	0.3574	-0.2618	0.4987	-3.3114	2.427	-32.4208
7	5.1615	-1.0046	2.2355	0.5336	-0.2283	1.1045	0.2045	0.4219	0.0764	-0.4005	-0.2067	0.0537	-0.1453	0.0505	0.0022	0.4399	0.2858	0.0597	0.5206	0.3626	0.3314	-69.9637	81.9067	-130.6922
8	5.0338	1.2417	4.9338	1.2086	1.404	4.9442	-0.0901	-0.2136	0.2488	-0.1038	-0.1309	0.3279	-0.2896	-0.3915	0.2211	0.3091	0.3389	0.2132	0.3871	0.2651	0.4985	-84.9615	85.016	-120.7257
9	0.5195	-0.3493	-1.1933	0.9992	2.0953	4.9507	-0.2372	0.0108	-0.3951	0.0598	-0.0665	-0.0812	0.4306	0.0131	0.3037	0.4866	0.3301	0.2646	0.2762	0.066	0.4724	-50.1029	45.4879	-114.1251
10	1.263	1.3729	1.1779	4.9894	5.0529	5.2738	-0.1602	0.3361	-0.0733	-0.3955	0.1739	-0.2407	-0.2002	0.2173	-0.0137	0.3505	0.2692	0.3193	0.4829	0.2675	0.3172	-46.9942	55.4421	-129.1227
11	1.1842	2.3938	-0.3205	5.2121	-1.0027	0.4745	0.0159	-0.1004	0.0815	0.117	0.1838	0.4431	0.0572	-0.3622	-0.1997	0.2734	0.0421	0.3028	0.4484	0.2899	0.4953	-86.5651	62.0449	-94.2857
12	5.3676	5.2587	1.4184	5.2551	1.23	1.2265	0.1607	-0.2948	-0.3842	0.1769	-0.0795	-0.2118	0.34	-0.099	-0.0812	0.4741	0.2477	0.252	0.3255	0.3476	0.3724	-76.589	47.0662	-91.1939

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	52 - 237
2	X-RAY DIFFRACTION	2	B	52 - 237
3	X-RAY DIFFRACTION	3	C	52 - 237
4	X-RAY DIFFRACTION	4	D	52 - 237
5	X-RAY DIFFRACTION	5	E	52 - 237
6	X-RAY DIFFRACTION	6	F	52 - 237
7	X-RAY DIFFRACTION	7	G	52 - 237
8	X-RAY DIFFRACTION	8	H	52 - 237
9	X-RAY DIFFRACTION	9	I	52 - 237
10	X-RAY DIFFRACTION	10	J	52 - 237
11	X-RAY DIFFRACTION	11	K	52 - 237
12	X-RAY DIFFRACTION	12	L	52 - 237

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Movie

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Structure viewers

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Open data

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Validation report

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Assembly

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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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