PDB-3kbo: 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW)...

ID or keywords:

Entry

Database: PDB / ID: 3kbo

Title

2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP

Components

Glyoxylate/hydroxypyruvate reductase A

Keywords

OXIDOREDUCTASE / NADP / NAD / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

hydroxypyruvate reductase (NADPH) activity / hydroxypyruvate reductase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.14 Å

Authors

Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Oct 20, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kbo.cif.gz	276.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3kbo.ent.gz	226.3 KB	Display	PDB format
PDBx/mmJSON format	3kbo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3kbo_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	3kbo_full_validation.pdf.gz	1.5 MB	Display
Data in XML	3kbo_validation.xml.gz	63 KB	Display
Data in CIF	3kbo_validation.cif.gz	81.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbo ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbo	HTTPS FTP

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Related structure data

Similar structure data	6sny-d 6ovl-1 4zph-2 4zqb-2 4n18-1 4mkr-1 5f8c-2 5jsc-4 6tz8-2 6p35-1 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
Other databases	TargetDB: idp00951

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Glyoxylate/hydroxypyruvate reductase A

B: Glyoxylate/hydroxypyruvate reductase A

C: Glyoxylate/hydroxypyruvate reductase A

D: Glyoxylate/hydroxypyruvate reductase A

hetero molecules

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

1

A: Glyoxylate/hydroxypyruvate reductase A

D: Glyoxylate/hydroxypyruvate reductase A

hetero molecules

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

2

B: Glyoxylate/hydroxypyruvate reductase A

C: Glyoxylate/hydroxypyruvate reductase A

hetero molecules

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

Unit cell

Length a, b, c (Å)	279.621, 45.585, 112.335
Angle α, β, γ (deg.)	90.00, 101.58, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Glyoxylate/hydroxypyruvate reductase A / 2-ketoacid reductase Mass: 35720.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: ghrA, STM1135, ycdW / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 References: UniProt: Q8ZQ30, glyoxylate reductase (NADP+), hydroxypyruvate reductase

#1: Protein

Glyoxylate/hydroxypyruvate reductase A / 2-ketoacid reductase

Mass: 35720.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: ghrA, STM1135, ycdW / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q8ZQ30, glyoxylate reductase (NADP+), hydroxypyruvate reductase

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Non-polymers , 5 types, 570 molecules

#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Chemical	ChemComp-NDB / N-(2-hydroxyethyl)-N,N-dimethyl-3-sulfopropan-1-aminium Mass: 212.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₈NO₄S
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	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: 2.45 Å³/Da / Density % sol: 49.88 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING ...Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING DROP, temperature 295K; Cryo: oil, paratone

Crystal

Density Matthews: 2.45 Å³/Da / Density % sol: 49.88 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.3M NDSB-211, 30% PEG 3350, 0.2M Sodium acetate, 0.1M Bis-Tris pH 6.5, 10mm NADP, VAPOR DIFFUSION, HANGING ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 13, 2009 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.14→30 Å / Num. all: 75710 / Num. obs: 75710 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 34.7 Å² / R_merge(I) obs: 0.084 / Net I/σ(I): 27
Reflection shell	Resolution: 2.14→2.18 Å / Redundancy: 6 % / R_merge(I) obs: 0.491 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3610 / % possible all: 93.5

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.14→29.93 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.934 / SU B: 9.853 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Individual Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26879	3806	5 %	RANDOM
R_work	0.21092	-	-	-
all	0.21387	71864	-	-
obs	0.21387	71864	98 %	-

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: 27.209 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.57 Å²	0 Å²	0.23 Å²
2-	-	5.13 Å²	-0 Å²
3-	-	-	-3.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→29.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9900	0	243	555	10698

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	10493
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7108
X-RAY DIFFRACTION	r_angle_refined_deg	1.453	1.982	14344
X-RAY DIFFRACTION	r_angle_other_deg	0.87	3	17228
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.762	5	1262
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.664	23.486	479
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.693	15	1667
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.682	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	1547
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	11583
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2149
X-RAY DIFFRACTION	r_mcbond_it	1.286	1.5	6290
X-RAY DIFFRACTION	r_mcbond_other	0.375	1.5	2514
X-RAY DIFFRACTION	r_mcangle_it	2.147	2	10124
X-RAY DIFFRACTION	r_scbond_it	3.469	3	4203
X-RAY DIFFRACTION	r_scangle_it	4.87	4.5	4220

LS refinement shell

Resolution: 2.14→2.199 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.323	232	-
R_work	0.297	4985	-
obs	-	4985	92.53 %

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	0.4603	0.1199	0.0061	0.3025	-0.2663	0.8941	0.0407	-0.0301	0.0403	-0.0344	-0.0227	0.0252	0.0268	0.0321	-0.018	0.0496	-0.0053	0.001	0.0054	0.0052	0.0522	19.3614	-0.9043	-21.2531
2	0.4393	0.1275	0.2623	0.0826	0.1668	0.355	-0.0341	0.0166	0.069	0.0058	-0.0062	0.0132	0.0011	-0.0237	0.0404	0.067	-0.0048	-0.0081	0.0126	0.0057	0.0714	22.6637	5.9603	9.5326
3	0.7817	0.2363	0.0179	0.2522	0.0759	0.4485	-0.0505	0.0279	0.1007	0.0243	0.0055	0.0498	-0.0099	-0.0879	0.045	0.0385	0.0118	-0.0173	0.0255	0.0025	0.0685	13.2476	7.1941	12.9317
4	0.0719	0.039	0.2087	0.2475	0.4228	1.2802	-0.0154	0.023	0.0438	-0.0195	0.0113	0.0055	0.0098	-0.0099	0.0041	0.0433	-0.0198	-0.0219	0.0316	0.0473	0.0751	20.0387	3.6112	-4.5158
5	0.3221	0.2222	-0.2963	0.9389	0.1876	0.8241	0.0293	-0.0703	0.0731	0.0645	0.0042	0.0274	-0.0567	0.0643	-0.0336	0.0418	-0.0209	0.0047	0.0581	-0.0057	0.0419	39.5714	18.5318	97.8761
6	0.1586	0.0361	0.0084	0.0417	-0.0518	0.2051	0.0205	0.0064	0.0094	-0.0175	0.0108	0.0195	-0.0177	0.036	-0.0313	0.0625	-0.0168	-0.0013	0.0307	0.0132	0.0671	28.0955	15.3626	66.6234
7	0.4886	0.0242	-0.0107	0.173	-0.0068	0.1908	0.0007	0.0447	0.0772	-0.0048	-0.0065	-0.0084	-0.026	0.0543	0.0059	0.0519	-0.0137	0.0026	0.0213	0.0104	0.0848	37.0521	22.6599	65.5416
8	0.4456	-0.1279	0.2327	0.1256	-0.1094	0.5672	0.0171	-0.0935	0.0528	-0.0157	0.0104	0.0275	-0.0023	0.0799	-0.0275	0.0401	-0.0031	0.0096	0.0615	-0.0185	0.0534	37.2591	13.6475	84.126
9	0.6511	0.0585	-0.276	0.0419	-0.1687	0.8172	-0.0051	-0.0111	0.0008	-0.0155	-0.0011	0.013	0.0046	0.0077	0.0062	0.0559	-0.0032	0.0013	0.0004	-0.0011	0.0645	5.6097	-1.958	35.8041
10	0.4477	0.158	0.046	0.1175	0.1278	0.2202	0.0079	-0.0227	0.0267	0.0007	-0.0103	0.0024	0.0076	-0.0169	0.0023	0.059	0.0005	-0.0052	0.0138	0.0024	0.0643	15.9008	11.59	70.1266
11	0.4181	0.0965	-0.1645	0.2208	-0.0425	0.2626	-0.0244	0.0594	0.0273	0.0236	0.0071	0.0267	-0.0181	-0.0337	0.0173	0.0529	0.0053	-0.0075	0.0148	0.0158	0.0651	2.831	8.6635	66.3382
12	0.0882	0.1188	0.1172	0.3444	0.0466	0.6907	0.021	-0.0586	-0.027	-0.0116	-0.0715	-0.0442	0.1325	0.0763	0.0505	0.0596	0.0076	0.0098	0.0955	0.0377	0.0537	10.7608	-8.9801	45.0105
13	0.603	0.4471	0.1124	0.5487	0.0149	0.9622	0.0533	-0.0162	0.0558	0.1272	-0.0091	0.0591	-0.0981	0.0294	-0.0442	0.0638	-0.0031	0.0304	0.0216	0.0063	0.0254	51.3144	18.6587	43.0773
14	0.4838	0.1694	0.3463	0.0727	0.1216	0.4524	-0.0374	0.0655	0.0352	-0.0243	0.0385	0.0381	-0.065	0.1146	-0.001	0.0635	-0.0217	-0.0133	0.0496	0.0256	0.0589	40.5427	14.9813	11.8914
15	0.7956	0.0714	-0.0301	0.3837	-0.0121	0.2979	-0.0981	0.0862	0.1595	-0.0501	0.0623	0.0432	-0.0596	0.1422	0.0358	0.0531	-0.0552	-0.0165	0.092	0.0366	0.0616	49.541	22.1541	10.4249
16	0.4832	0.144	0.4329	0.0435	0.1296	0.4066	-0.0308	-0.0012	0.0468	-0.0123	0.0017	0.016	-0.0289	0.0311	0.0291	0.0387	0.0037	0.0123	0.0622	-0.0033	0.0638	48.68	14.6819	28.7217
17	0.6004	0.3334	-0.883	0.2038	-0.6689	3.0135	-0.0712	0.1367	0.0865	-0.0261	0.0669	0.035	-0.0046	-0.1095	0.0043	0.0677	-0.0053	-0.0041	0.0467	0.0141	0.0831	16.5018	-0.63	2.8276
18	4.2694	0.6566	-1.8605	0.1231	-0.1718	1.4117	0.0844	-0.0217	0.1582	-0.0092	-0.0107	0.021	-0.1618	-0.0076	-0.0737	0.0519	-0.0141	0.0032	0.0509	0.0029	0.0635	41.0249	16.7092	75.4442
19	0.5569	-0.2558	0.5416	0.1176	-0.2484	0.5531	-0.0135	0.0522	-0.0137	0.0093	-0.0202	0.0081	-0.0136	0.0219	0.0337	0.0762	-0.0047	0.0065	0.0637	-0.0314	0.089	4.459	-0.2433	57.6877
20	0.1802	-0.2529	-0.4965	0.3628	0.7687	2.0339	0.007	0.0155	-0.0333	-0.0288	-0.0042	0.0364	-0.1659	0.1398	-0.0028	0.0801	-0.0285	-0.0004	0.0738	-0.0083	0.057	53.0104	16.601	20.5402
21	0.0025	0.0698	-0.35	1.9495	-9.7611	48.8807	0.0315	-0.0002	-0.0003	0.1364	0.0672	0.0271	-0.7029	-0.1774	-0.0987	0.0929	-0.0794	-0.0135	0.1399	0.0193	0.1383	7.1775	-3.1945	-26.9217
22	47.2468	6.0695	16.3438	1.8329	1.9938	5.6646	-0.3557	3.5729	0.4398	0.0239	0.2377	0.3585	-0.1285	1.2655	0.118	0.1261	-0.0647	0.0142	0.5244	0.065	0.1687	37.284	1.5995	11.9784
23	6.6552	9.7576	19.0642	14.3186	28.5642	99.5559	0.2652	1.0913	-0.5463	0.3117	1.6264	-0.7877	-1.7358	3.1819	-1.8916	0.2277	0.0233	-0.0409	0.1992	-0.0371	0.1869	25.4828	1.9707	66.6664

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 67
2	X-RAY DIFFRACTION	2	A	68 - 170
3	X-RAY DIFFRACTION	3	A	171 - 255
4	X-RAY DIFFRACTION	4	A	256 - 312
5	X-RAY DIFFRACTION	5	B	1 - 79
6	X-RAY DIFFRACTION	6	B	80 - 156
7	X-RAY DIFFRACTION	7	B	157 - 265
8	X-RAY DIFFRACTION	8	B	266 - 312
9	X-RAY DIFFRACTION	9	C	1 - 90
10	X-RAY DIFFRACTION	10	C	91 - 156
11	X-RAY DIFFRACTION	11	C	157 - 279
12	X-RAY DIFFRACTION	12	C	280 - 312
13	X-RAY DIFFRACTION	13	D	1 - 79
14	X-RAY DIFFRACTION	14	D	80 - 157
15	X-RAY DIFFRACTION	15	D	158 - 263
16	X-RAY DIFFRACTION	16	D	264 - 312
17	X-RAY DIFFRACTION	17	A	313
18	X-RAY DIFFRACTION	18	B	313
19	X-RAY DIFFRACTION	19	C	313
20	X-RAY DIFFRACTION	20	D	313
21	X-RAY DIFFRACTION	21	A	314
22	X-RAY DIFFRACTION	22	D	314
23	X-RAY DIFFRACTION	23	B	314

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 570 molecules

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-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 570 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

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This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 570 molecules

-
Details

-
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

-
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)

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Jul 12, 2017. Major update of PDB

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Yorodumi