PDB-4wgh: Crystal structure of aldo/keto reductase from Klebsiella pneumoni...

ID or keywords:

Entry

Database: PDB / ID: 4wgh

Title

Crystal structure of aldo/keto reductase from Klebsiella pneumoniae in complex with NADP and acetate at 1.8 A resolution

Components

Aldehyde reductase

Keywords

OXIDOREDUCTASE / Aldo/keto reductase / NADP / Klebsiella pneumoniae / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium

Function / homology

NADP-dependent oxidoreductase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :

Function and homology information

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Bacal, P. / Shabalin, I.G. / Cooper, D.R. / Hillerich, B.S. / Zimmerman, M.D. / Chowdhury, S. / Hammonds, J. / Al Obaidi, N. / Gizzi, A. / Bonanno, J. ...

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal structure of aldo/keto reductase from Klebsiella pneumoniae in complex with NADP and acetate at 1.8 A resolution
Authors: Bacal, P. / Shabalin, I.G. / Cooper, D.R. / Hillerich, B.S. / Zimmerman, M.D. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.

History

Deposition	Sep 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2015	Group: Data collection
Revision 1.2	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author / database_2 Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5	Dec 27, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4wgh.cif.gz	135.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4wgh.ent.gz	104.7 KB	Display	PDB format
PDBx/mmJSON format	4wgh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4wgh_validation.pdf.gz	711.9 KB	Display	wwPDB validaton report
Full document	4wgh_full_validation.pdf.gz	712.5 KB	Display
Data in XML	4wgh_validation.xml.gz	14.9 KB	Display
Data in CIF	4wgh_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/4wgh ftp://data.pdbj.org/pub/pdb/validation_reports/wg/4wgh	HTTPS FTP

-
Related structure data

Similar structure data	3wbw-1 1mzr-1 6cia-d 7d5j-1 1jb4-d 5gp1-1 3b3d-2 1xxg-d 5c7h-d 2wk0-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYSGRC-013574

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aldehyde reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	99.483, 99.483, 55.181
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	171
Space group name H-M	P6₂

Components on special symmetry positions

ID	Model	Components
1	1	A-455- HOH

Details

biological unit is the same as asym.

#1: Protein	Aldehyde reductase Mass: 34768.977 Da / Num. of mol.: 1 / Mutation: T279N Source method: isolated from a genetically manipulated source Details: Mutatation: T279N / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: L364_03163, WP_004176538.1 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: V3S9R5
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.55 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.45 ul of 13 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 30mM NADP were mixed with 0.45 ul of 2.8 M Sodium Acetate pH 6.2 and ...Details: 0.45 ul of 13 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 30mM NADP were mixed with 0.45 ul of 2.8 M Sodium Acetate pH 6.2 and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci).

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 46.55 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.45 ul of 13 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 30mM NADP were mixed with 0.45 ul of 2.8 M Sodium Acetate pH 6.2 and ...

-
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: Mar 20, 2014 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 56317 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 28.4 Å² / R_merge(I) obs: 0.048 / R_pim(I) all: 0.028 / R_rim(I) all: 0.056 / Χ²: 0.978 / Net I/av σ(I): 27.4 / Net I/σ(I): 10.2 / Num. measured all: 218509

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.8-1.83	3.7	0.62	1.43	2809	0.726	0.369	0.723	0.649	97.3
1.83-1.86	3.8	0.516		2786	0.803	0.307	0.604	0.659	98.4
1.86-1.9	3.9	0.457		2781	0.819	0.27	0.534	0.664	98.3
1.9-1.94	3.9	0.337		2778	0.9	0.199	0.394	0.677	99.5
1.94-1.98	3.9	0.293		2834	0.919	0.172	0.341	0.686	98.5
1.98-2.03	3.9	0.222		2841	0.959	0.13	0.258	0.695	99.4
2.03-2.08	3.9	0.188		2787	0.968	0.11	0.219	0.709	99.3
2.08-2.13	3.9	0.144		2817	0.98	0.084	0.167	0.702	98.9
2.13-2.2	3.9	0.115		2848	0.987	0.067	0.134	0.717	99.5
2.2-2.27	3.9	0.113		2803	0.984	0.066	0.131	0.754	99.6
2.27-2.35	3.9	0.088		2796	0.992	0.051	0.102	0.793	99.2
2.35-2.44	3.9	0.074		2834	0.995	0.042	0.085	0.837	99.5
2.44-2.55	3.9	0.069		2822	0.995	0.039	0.08	0.887	99.5
2.55-2.69	3.9	0.055		2845	0.997	0.031	0.063	0.937	99.6
2.69-2.86	3.9	0.047		2830	0.997	0.027	0.055	1.06	99.7
2.86-3.08	3.9	0.043		2841	0.998	0.024	0.049	1.204	99.6
3.08-3.39	3.9	0.041		2805	0.997	0.023	0.047	1.577	99.9
3.39-3.88	3.9	0.036		2836	0.998	0.02	0.041	1.778	99.8
3.88-4.88	3.9	0.032		2848	0.998	0.018	0.037	1.755	99.9
4.88-50	3.8	0.03		2776	0.998	0.018	0.035	1.789	97.4

-
Processing

Software

Name	Version	Classification
Blu-Ice		data collection
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
DM		phasing
MLPHARE		phasing
REFMAC	5.8.0073	refinement
PDB_EXTRACT	3.15	data extraction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.8→50 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.967 / WR_factor R_free: 0.1904 / WR_factor R_work: 0.1449 / FOM work R set: 0.8622 / SU B: 5.303 / SU ML: 0.082 / SU R Cruickshank DPI: 0.0989 / SU R_free: 0.1016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.102 / SU R_free Cruickshank DPI: 0.1016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1854	1473	5.1 %	RANDOM
R_work	0.1446	27524	-	-
obs	0.1466	27524	99.87 %	-

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 max: 95.99 Å² / B_iso mean: 38.07 Å² / B_iso min: 19.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.17 Å²	-0.59 Å²	-0 Å²
2-	-	-1.17 Å²	0 Å²
3-	-	-	3.8 Å²

Refinement step

Cycle: final / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2166	0	52	227	2445
B_iso mean	-	-	30.24	43.96	-
Num. residues	-	-	-	-	283

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	2287
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2163
X-RAY DIFFRACTION	r_angle_refined_deg	1.654	1.985	3126
X-RAY DIFFRACTION	r_angle_other_deg	0.846	3	4938
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.831	5	288
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.649	23.434	99
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.033	15	333
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.887	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	351
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	2603
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	534
X-RAY DIFFRACTION	r_mcbond_it	1.02	1.511	1138
X-RAY DIFFRACTION	r_mcbond_other	1.012	1.507	1136
X-RAY DIFFRACTION	r_mcangle_it	1.51	2.256	1421

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	96	-
R_work	0.255	2057	-
all	-	2153	-
obs	-	-	99.95 %

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	2.8134	0.3088	-0.3815	7.2962	4.3948	5.4163	-0.0999	-0.2267	-0.2555	0.2612	0.1496	-0.8079	0.5407	0.3461	-0.0498	0.1177	0.0399	0.0057	0.142	0.1131	0.239	71.654	8.957	11.875
2	8.5292	1.0147	1.4184	3.378	0.7934	2.084	-0.1394	0.5514	0.2487	-0.6713	0.026	0.4571	0.0039	-0.1801	0.1134	0.2256	-0.0237	-0.0742	0.1601	0.0515	0.0852	50.56	13.304	-0.358
3	1.6282	0.5912	0.009	3.0093	0.3398	0.7578	0.0282	0.0629	-0.1474	-0.1559	-0.0906	0.0052	0.1967	-0.0985	0.0624	0.1956	-0.0277	-0.0061	0.1532	0.04	0.0538	55.398	9.043	5.654
4	3.3492	3.1016	-0.3042	10.8023	-2.6195	5.0839	-0.0793	-0.058	0.2443	-0.1668	0.0025	0.5086	0.1186	-0.3985	0.0768	0.1149	-0.0121	-0.0187	0.1715	0.0157	0.0762	49.129	14.769	7.754
5	21.7289	8.1187	1.3292	3.8014	-0.7969	8.7019	-0.0191	-0.198	-0.6513	-0.0336	-0.1944	-0.2277	0.7853	-0.193	0.2135	0.195	0.0001	0.0467	0.1286	0.0471	0.0769	54.557	6.267	16.753
6	0.3208	0.1493	-0.5717	7.0032	-2.1122	2.0685	0.0835	-0.1028	0.0522	-0.0156	-0.1	0.0508	-0.0765	0.0568	0.0165	0.119	-0.014	-0.0078	0.1606	0.0136	0.1023	58.244	24.866	9.965
7	19.2017	7.5037	-0.6057	28.6544	1.4678	0.1321	0.2182	-0.3643	0.4841	1.0531	-0.2143	0.3709	0.0544	0.0104	-0.0039	0.302	-0.029	0.0208	0.237	0.0078	0.0926	54.855	29.993	16.427
8	0.8198	0.4684	-1.2049	3.75	-1.9238	3.4334	0.0204	-0.0509	0.0259	0.162	-0.0599	-0.0333	-0.0766	-0.0809	0.0395	0.1192	-0.0167	-0.0161	0.1437	0.0155	0.0549	56.364	21.765	12.92
9	1.9286	1.2417	-0.6002	5.881	-2.9875	4.3721	0.0749	-0.3028	0.2592	0.5862	-0.15	-0.1194	-0.423	0.0589	0.0751	0.1826	-0.0438	-0.0676	0.1723	-0.0038	0.0763	63.678	31.343	17.534
10	1.311	0.0464	-0.6835	2.2586	0.2533	2.3954	-0.0021	-0.1511	0.0849	-0.1419	-0.1207	-0.706	-0.1606	0.3074	0.1229	0.1265	-0.021	0.0226	0.1969	0.1092	0.2792	72.284	24.412	6.264
11	3.5204	-1.0402	0.9218	1.3022	5.3735	32.7349	-0.0358	-0.1993	0.1133	-0.0441	0.1531	-0.168	-0.1093	0.6207	-0.1172	0.2139	0.0027	0.2343	0.2606	0.1783	0.8931	80.444	22.572	1.796
12	4.1627	0.453	-1.0795	2.1499	-0.743	1.9715	-0.0203	-0.24	0.1161	-0.1954	-0.2242	-0.5746	0.1288	0.1234	0.2445	0.1344	0.0317	0.0801	0.1258	0.1204	0.2304	71.513	17.397	2.558
13	9.9316	19.2324	-1.455	38.0645	-5.6131	9.931	-1.018	0.718	0.5472	-1.7067	1.4738	1.1192	-0.6091	-0.6223	-0.4559	0.6503	0.0632	0.1232	0.5139	0.2662	0.3677	62.009	14.635	-11.92
14	7.0676	-7.9652	2.6287	12.8989	-8.8499	10.1485	0.4926	0.8745	0.6536	-0.4701	-0.1277	-0.3355	-0.5468	-0.6642	-0.3649	1.0762	-0.5014	0.0783	1.0614	0.1513	0.413	67.996	8.241	-17.699
15	7.1873	-7.2095	-5.1433	31.674	1.2975	5.7402	-0.4737	0.7581	-0.038	-1.2868	0.4731	-1.479	0.2242	-0.1123	0.0006	0.5275	-0.1505	0.2488	0.5105	-0.1362	0.2449	72.853	-0.03	-15.824
16	4.5403	1.1977	-0.1069	6.702	2.6014	4.6307	-0.1612	0.3408	0.0627	-0.3804	-0.0653	-0.3987	0.4187	0.2139	0.2265	0.2401	0.0336	0.1889	0.1136	0.0688	0.1732	72.464	4.644	-5.614
17	7.0848	1.9385	1.3311	3.7796	1.2969	2.093	-0.1189	0.1341	0.1308	-0.3734	-0.071	-0.202	0.2723	0.0004	0.1899	0.1966	0.0006	0.0636	0.1285	0.0704	0.0856	63.459	8.05	0.361
18	4.9856	-0.1912	-0.6872	1.6855	-0.229	1.5021	-0.2452	0.1073	-0.5135	-0.4772	0.0773	-0.6125	0.3357	0.0688	0.1679	0.2992	0.0252	0.2054	0.144	0.0129	0.3175	72.935	2.325	-4.818
19	10.5851	9.4913	-3.671	12.6941	-0.0999	6.2511	0.0347	0.942	0.6123	-0.0484	0.2011	-0.3592	0.5706	0.1047	-0.2358	0.4219	0.145	0.3523	0.5649	0.3538	0.5629	80.768	17.448	-13.007
20	24.3431	5.9327	8.4969	22.2485	-4.4158	10.3711	0.2836	1.2892	1.1551	-0.6667	-0.1126	0.2164	0.1551	0.0931	-0.171	0.252	0.0958	0.1915	0.2153	0.1965	0.257	70.352	26.318	-6.939

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 17
2	X-RAY DIFFRACTION	2	A	18 - 31
3	X-RAY DIFFRACTION	3	A	32 - 56
4	X-RAY DIFFRACTION	4	A	57 - 67
5	X-RAY DIFFRACTION	5	A	68 - 74
6	X-RAY DIFFRACTION	6	A	75 - 88
7	X-RAY DIFFRACTION	7	A	89 - 95
8	X-RAY DIFFRACTION	8	A	96 - 116
9	X-RAY DIFFRACTION	9	A	117 - 135
10	X-RAY DIFFRACTION	10	A	136 - 176
11	X-RAY DIFFRACTION	11	A	177 - 184
12	X-RAY DIFFRACTION	12	A	185 - 197
13	X-RAY DIFFRACTION	13	A	198 - 203
14	X-RAY DIFFRACTION	14	A	204 - 210
15	X-RAY DIFFRACTION	15	A	211 - 218
16	X-RAY DIFFRACTION	16	A	219 - 234
17	X-RAY DIFFRACTION	17	A	235 - 247
18	X-RAY DIFFRACTION	18	A	248 - 269
19	X-RAY DIFFRACTION	19	A	270 - 278
20	X-RAY DIFFRACTION	20	A	279 - 284

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
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

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-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

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
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

-
Yorodumi