PDB-5c41: Crystal structure of human ribokinase in complex with AMPPCP in P...

ID or keywords:

Entry

Database: PDB / ID: 5c41

Title

Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers

Components

Ribokinase

Keywords

TRANSFERASE

Function / homology

Function and homology information

ribokinase /

ribokinase activity /

Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt /

ATP binding / identical protein binding /

metal ion binding /

nucleus /

cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Park, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.

Citation

Journal: To Be Published
Title: Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers
Authors: Park, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.

History

Deposition	Jun 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 15, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2017	Group: Database references / Structure summary
Revision 1.2	Sep 27, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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	5c41.cif.gz	505.7 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c4/5c41 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/5c41	HTTPS FTP

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Related structure data

Related structure data	2fv7S 5byc 5byd 5bye 5byf 5c3y 5c3z 5c40 S: Starting model for refinement
Similar structure data	6wk0-1 3i3y-2 7agh-2 3i3y-1 3ikh-1 3b1q-2 4pvv-1 1v1a-d 2c49-d 4kpn-1 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	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Ribokinase

B: Ribokinase

C: Ribokinase

D: Ribokinase

hetero molecules

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

1

A: Ribokinase

B: Ribokinase

hetero molecules

defined by author&software
71.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Ribokinase

D: Ribokinase

hetero molecules

defined by author&software
71.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.950, 89.190, 144.400
Angle α, β, γ (deg.)	90.00, 98.16, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	LEU	LEU	A	A	15 - 323	15 - 323
2	1	VAL	VAL	LEU	LEU	B	B	15 - 323	15 - 323
1	2	GLU	GLU	HIS	HIS	A	A	14 - 330	14 - 330
2	2	GLU	GLU	HIS	HIS	C	C	14 - 330	14 - 330
1	3	GLU	GLU	HIS	HIS	A	A	14 - 328	14 - 328
2	3	GLU	GLU	HIS	HIS	D	D	14 - 328	14 - 328
1	4	VAL	VAL	LEU	LEU	B	B	15 - 323	15 - 323
2	4	VAL	VAL	LEU	LEU	C	C	15 - 323	15 - 323
1	5	VAL	VAL	LEU	LEU	B	B	15 - 323	15 - 323
2	5	VAL	VAL	LEU	LEU	D	D	15 - 323	15 - 323
1	6	GLU	GLU	HIS	HIS	C	C	14 - 328	14 - 328
2	6	GLU	GLU	HIS	HIS	D	D	14 - 328	14 - 328

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Ribokinase / Mass: 35241.008 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBKS, RBSK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H477, ribokinase
#2: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1004 / 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: 2.35 Å³/Da / Density % sol: 47.64 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium HEPES, 10% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 1.95→44.55 Å / Num. obs: 94826 / % possible obs: 99.8 % / Redundancy: 3.8 % / B_iso Wilson estimate: 13.018 Å² / R_merge(I) obs: 0.096 / Net I/σ(I): 11.1
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.727 / Mean I/σ(I) obs: 1.9 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0123	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FV7

2fv7

Resolution: 1.95→44.55 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.94 / SU B: 8.242 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20733	4824	5.1 %	RANDOM
R_work	0.17215	-	-	-
obs	0.17394	89981	99.75 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.604 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.87 Å²	0 Å²	-0.22 Å²
2-	-	-0.18 Å²	0 Å²
3-	-	-	-0.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→44.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9310	0	137	1004	10451

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.019	9748
X-RAY DIFFRACTION	r_bond_other_d	0.014	0.02	9252
X-RAY DIFFRACTION	r_angle_refined_deg	2.011	1.983	13324
X-RAY DIFFRACTION	r_angle_other_deg	2.073	3	21286
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.349	5	1285
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.473	25.341	367
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.84	15	1545
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.055	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	1606
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	11149
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	2087
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	0.693	1.092	5110
X-RAY DIFFRACTION	r_mcbond_other	0.692	1.091	5109
X-RAY DIFFRACTION	r_mcangle_it	1.138	1.633	6405
X-RAY DIFFRACTION	r_mcangle_other	1.138	1.633	6406
X-RAY DIFFRACTION	r_scbond_it	1.235	1.268	4638
X-RAY DIFFRACTION	r_scbond_other	1.224	1.266	4635
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.908	1.853	6914
X-RAY DIFFRACTION	r_long_range_B_refined	6.491	10.666	11462
X-RAY DIFFRACTION	r_long_range_B_other	6.304	9.66	10938
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	35506	0.12
1	2	B	35506	0.12
2	1	A	37074	0.1
2	2	C	37074	0.1
3	1	A	36584	0.1
3	2	D	36584	0.1
4	1	B	35056	0.13
4	2	C	35056	0.13
5	1	B	35042	0.12
5	2	D	35042	0.12
6	1	C	35664	0.11
6	2	D	35664	0.11

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.289	338	-
R_work	0.278	6576	-
obs	-	-	98.79 %

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	2.1468	-1.1053	-2.1286	1.2449	0.2648	3.1662	-0.0403	-0.111	0.1453	0.2153	0.146	-0.0866	-0.1624	-0.043	-0.1057	0.1025	-0.0188	0.0294	0.0811	-0.0163	0.0934	-3.8292	3.0814	75.1308
2	2.1573	-0.5296	-0.9723	1.9163	0.5862	2.9537	-0.0648	-0.1515	-0.0919	0.2647	0.0119	0.0479	0.1343	0.069	0.0529	0.0997	-0.014	0.0295	0.0291	0.0232	0.0491	0.7528	-7.74	73.2055
3	3.4574	0.0377	0.118	1.0367	-0.6523	1.6833	-0.0212	-0.1101	0.0013	0.1242	-0.0779	-0.1408	-0.1277	0.1673	0.099	0.062	-0.0195	0.0089	0.0223	0.0086	0.0365	12.7561	3.5633	62.7865
4	9.4408	-3.5978	-4.978	1.3919	1.771	3.4252	0.4797	0.2852	0.7218	-0.1701	-0.1228	-0.272	-0.2213	0.2018	-0.3568	0.2849	-0.0208	0.0018	0.3416	0.0524	0.2074	10.7232	7.6794	47.0783
5	1.9975	-1.0679	-1.8501	2.3795	0.5983	3.9267	-0.095	-0.0513	-0.0666	-0.0277	0.0571	-0.1561	0.1103	0.1508	0.0379	0.1632	-0.0064	0.0112	0.0079	-0.0048	0.0245	-13.9733	5.5052	96.0743
6	2.87	-0.8303	-0.6047	3.4196	-0.2122	2.7031	-0.056	-0.0572	-0.0498	-0.1659	0.1314	0.0435	0.0494	-0.137	-0.0753	0.1607	-0.0294	0.0064	0.0181	0.0039	0.0051	-21.226	11.5939	90.9437
7	1.8776	0.0445	-0.1519	4.8221	0.1871	4.7344	-0.1772	-0.116	0.3134	0.0012	0.0763	0.3168	-0.4746	-0.4499	0.101	0.2411	0.0945	-0.0127	0.0611	-0.0197	0.0796	-25.5068	21.6909	103.4295
8	0.954	-0.3432	0.0269	3.7413	0.3431	2.6213	-0.1634	-0.1906	0.0364	0.3698	0.1532	-0.197	-0.0464	0.0408	0.0102	0.212	0.0809	0.0042	0.0802	0.0013	0.0167	-15.5725	11.0144	113.5663
9	2.3392	1.3602	2.0303	2.4207	-0.3335	3.4317	0.0394	0.1296	-0.1953	-0.4603	0.2807	0.1185	0.3731	-0.1195	-0.3202	0.2006	-0.0558	-0.0852	0.1432	0.0826	0.1597	24.1075	10.2097	33.4121
10	2.4511	-0.0406	1.082	3.7807	-0.2531	3.5778	-0.0808	-0.0013	0.0277	-0.3255	0.3046	0.3929	-0.0644	-0.3083	-0.2238	0.0812	-0.046	-0.0497	0.1977	0.1318	0.1743	20.9398	21.0665	32.0344
11	2.4481	-0.3941	0.4679	1.6955	-1.1317	2.4344	-0.0381	0.1312	0.0611	-0.1306	0.016	-0.0462	-0.0243	0.0317	0.0221	0.0806	-0.0267	0.0049	0.0161	0.0067	0.0206	38.3566	17.8853	41.3141
12	10.322	3.3046	1.6628	3.9581	1.0016	3.2759	0.1468	-0.3112	-0.1908	0.148	0.0356	-0.2401	0.1181	0.2749	-0.1825	0.0918	-0.0026	0.0154	0.1673	0.0694	0.0944	31.3313	8.924	58.1346
13	3.7513	4.8554	2.1361	6.3469	3.1652	3.9509	-0.0553	0.0645	-0.2593	-0.1284	0.1932	-0.3393	-0.1397	0.5679	-0.1379	0.408	-0.0668	-0.1	0.269	0.0766	0.2095	19.619	6.5162	15.1142
14	1.3367	0.8387	0.3831	3.3648	0.4935	4.1091	0.1912	-0.1112	-0.1382	0.2301	-0.1232	-0.1808	0.3667	-0.0048	-0.068	0.3683	-0.0551	-0.0685	0.1377	0.064	0.0588	7.656	-5.0329	12.2665
15	2.4862	-0.2286	0.375	3.8363	-0.0053	4.5193	0.1707	0.3344	-0.3771	-0.2266	-0.0308	-0.8505	0.6174	0.8212	-0.1399	0.4668	0.1007	0.0042	0.3338	0.0059	0.2952	16.4489	-8.0947	-4.8215
16	1.9304	0.5437	2.5748	0.9473	2.3267	9.219	0.0755	-0.0491	0.0463	-0.047	-0.2119	-0.0399	-0.2969	-0.4382	0.1365	0.2994	0.0019	0.0164	0.1522	0.0853	0.1097	4.6454	4.622	-9.9544

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 77
2	X-RAY DIFFRACTION	2	A	78 - 189
3	X-RAY DIFFRACTION	3	A	190 - 323
4	X-RAY DIFFRACTION	4	A	324 - 330
5	X-RAY DIFFRACTION	5	B	15 - 68
6	X-RAY DIFFRACTION	6	B	69 - 136
7	X-RAY DIFFRACTION	7	B	137 - 184
8	X-RAY DIFFRACTION	8	B	185 - 324
9	X-RAY DIFFRACTION	9	C	14 - 68
10	X-RAY DIFFRACTION	10	C	69 - 143
11	X-RAY DIFFRACTION	11	C	144 - 314
12	X-RAY DIFFRACTION	12	C	315 - 330
13	X-RAY DIFFRACTION	13	D	14 - 50
14	X-RAY DIFFRACTION	14	D	51 - 186
15	X-RAY DIFFRACTION	15	D	187 - 307
16	X-RAY DIFFRACTION	16	D	308 - 329

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-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

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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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

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Yorodumi