PDB-9c5i: Trypanosoma cruzi beta-3-HBDH APO structure (C2 space group)

ID or keywords:

Entry

Database: PDB / ID: 9c5i

Title

Trypanosoma cruzi beta-3-HBDH APO structure (C2 space group)

Components

Hydroxybutyrate dehydrogenase

Keywords

OXIDOREDUCTASE / Trypanosoma cruzi / NADPH / malonate / beta-3-Hydroxybutyrate dehydrogenase

Function / homology

Function and homology information

3-hydroxybutyrate dehydrogenase activity / monocarboxylic acid metabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase / lipid metabolic process
Similarity search - Function

Biological species

Trypanosoma cruzi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Hashimoto, H. / Debler, E.W.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Trypanosoma cruzi D-3-hydroxybutyrate dehydrogenase (HBDH) is NADP-dependent enzyme.
Authors: Hashimoto, H. / Debler, E.W.

History

Deposition	Jun 6, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9c5i.cif.gz	609.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9c5i.ent.gz	472.3 KB	Display	PDB format
PDBx/mmJSON format	9c5i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9c5i_validation.pdf.gz	448.2 KB	Display	wwPDB validaton report
Full document	9c5i_full_validation.pdf.gz	453.6 KB	Display
Data in XML	9c5i_validation.xml.gz	40.3 KB	Display
Data in CIF	9c5i_validation.cif.gz	51.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/9c5i ftp://data.pdbj.org/pub/pdb/validation_reports/c5/9c5i	HTTPS FTP

-
Related structure data

Related structure data	9c5hC 9c5jC 9c5kC 9c5lC 9c5mC 9c5nC 9c5oC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (3) #90 - Jun 2007 Fatty Acid Synthase similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (3) #77 - May 2006 Glucose Oxidase similarity (2)

Deposited unit

A: Hydroxybutyrate dehydrogenase

B: Hydroxybutyrate dehydrogenase

C: Hydroxybutyrate dehydrogenase

D: Hydroxybutyrate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	119.610, 80.060, 122.220
Angle α, β, γ (deg.)	90.000, 107.000, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Hydroxybutyrate dehydrogenase Mass: 28617.025 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: genomic DNA / Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Sylvio X10/1 / Gene: C4B63_13g310 / Plasmid: pED624 / Details (production host): His-3C-TcHBDH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RIL-codon plus / References: UniProt: A0A2V2VPF1
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.68 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M NaCl, 20% PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2022
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.8→47.79 Å / Num. obs: 27427 / % possible obs: 99.6 % / Redundancy: 3.8 % / B_iso Wilson estimate: 63.66 Å² / CC_1/2: 0.986 / R_merge(I) obs: 0.132 / Net I/σ(I): 12.3
Reflection shell	Resolution: 2.8→2.87 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.673 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2048 / CC_1/2: 0.773 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→47.79 Å / SU ML: 0.3685 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2449	1367	5 %	Random
R_work	0.2133	25949	-	-
obs	0.215	27316	99.7 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 71.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→47.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7618	0	4	52	7674

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0027	7735
X-RAY DIFFRACTION	f_angle_d	0.4951	10482
X-RAY DIFFRACTION	f_chiral_restr	0.0433	1239
X-RAY DIFFRACTION	f_plane_restr	0.0039	1352
X-RAY DIFFRACTION	f_dihedral_angle_d	12.0862	2781

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.8-2.9	0.3379	136	0.3432	2590	X-RAY DIFFRACTION	99.67
2.9-3.02	0.3053	135	0.2904	2546	X-RAY DIFFRACTION	99.81
3.02-3.15	0.3165	136	0.2896	2589	X-RAY DIFFRACTION	99.71
3.15-3.32	0.3311	136	0.2949	2603	X-RAY DIFFRACTION	99.64
3.32-3.53	0.2728	135	0.2348	2546	X-RAY DIFFRACTION	99.78
3.53-3.8	0.2709	138	0.211	2613	X-RAY DIFFRACTION	99.89
3.8-4.18	0.2499	136	0.2096	2598	X-RAY DIFFRACTION	99.78
4.18-4.79	0.1982	136	0.1743	2593	X-RAY DIFFRACTION	99.71
4.79-6.03	0.2162	138	0.1911	2612	X-RAY DIFFRACTION	99.75
6.03-47.79	0.2031	141	0.1724	2659	X-RAY DIFFRACTION	99.4

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	8.43514300372	-0.96084765026	2.65342746513	4.62332603439	0.695127350976	2.5581674044	0.142841842798	1.32921536564	0.0424380328306	-0.644857473895	-0.0300986123604	-0.42573429719	-0.457913344907	-0.172488348294	-0.0565946293655	0.924553442938	-0.00316861033314	-0.0498200497603	0.590707402508	0.02781527814	0.449850040454	26.9721057606	14.4174905488	11.9506862073
2	7.91938044933	-3.07876835652	5.8155909391	4.67176017045	-2.54042877207	4.73435229977	-0.239674877329	0.920791969849	-0.751609917996	-0.355673598529	0.0140212351354	0.0842668790688	-0.409993699283	0.620798474766	0.33334400878	0.809295908408	-0.0985596062758	0.0247484005107	0.607119733076	0.0870890541485	0.48901796898	30.0634959731	18.0651071222	7.10286781789
3	2.93940480825	-3.53407565174	-1.56219108016	7.7568428891	0.616494660489	2.27388899866	-0.0794015425903	0.309488686829	0.622947495374	-0.327795160545	-0.0381338847689	-1.22573896756	-0.357401641198	0.376131221193	0.103750822432	0.931480887777	-0.218860777202	-0.117542766995	0.798524602181	0.0733435324855	0.616884993594	39.1033364867	12.1765809717	15.8747944474
4	6.4272040982	-6.85416140833	-3.43334786016	8.68132283157	4.97034796251	5.21901198429	0.67922557716	0.127307321424	1.02229706056	-1.01402100124	-0.26717207206	-1.36779137091	-1.02010057797	0.499701477036	-0.149626509755	0.754928692183	-0.169803952231	-0.076132926033	0.659562399807	0.209653263028	0.606810139444	41.0891919564	11.403662842	22.2029601151
5	2.46679346252	-1.53155082885	0.443274254061	3.38316644867	-2.36666885664	2.35439059817	-0.0771758865643	0.150515634787	0.108245764111	0.185820980743	-0.0482980212809	-0.0489156521324	-0.112995840783	-0.0412938714208	0.0670487760633	0.464931163914	-0.119630068965	-0.0903548179021	0.457110391454	0.00547609718124	0.320200141487	33.460935	2.3787230943	23.1569783795
6	5.33677231324	-2.49849639597	-4.49376230516	1.62000811523	0.944041864268	9.09775266212	0.115982221569	0.0111776070339	0.0570787712327	0.553891053975	0.0962912033494	0.108945326789	-0.309082734674	0.128603089199	-0.322846230272	0.952405284216	0.0108872802098	-0.0491225554498	0.658233499273	-0.100530617647	0.625427782603	33.7634779709	-10.4649476135	0.842717243197
7	1.99507503285	-0.495233388821	0.541282043747	3.58719000407	-1.67901906455	1.51564902455	-0.0711576106382	0.0734686287572	0.00194602434288	-0.213700758663	0.1455079554	0.360985020875	0.097154347515	-0.00214731516365	-0.12428251	0.634729036846	-0.0450616922152	0.00815063204632	0.508143093736	-0.0193656283824	0.367354932651	24.103420706	-1.49670938184	19.4157297027
8	4.37497450155	4.29856455266	-3.4669740345	4.7295530695	-3.91660286702	9.44484543011	0.199229989051	-0.413659007429	0.461466733008	0.953110445669	0.572624948189	0.987584446419	-1.93517502842	0.0161764255746	-0.631632455137	0.822273489149	0.102091384411	-0.157969717243	0.758008628727	0.136156476661	0.848648276144	2.82332658836	-1.95191230192	26.6532250778
9	9.62549554133	2.95013522932	-4.61386145129	3.53714904585	0.325502242155	3.35714272905	0.0530908372356	-0.863325709071	0.0660828233349	0.773738914277	-0.273797004879	0.035501317754	-0.695129632846	-0.470835987691	0.190605241184	0.45046022706	0.0713137142145	-0.177436236231	0.606602224398	-0.00817006980624	0.584254122474	-0.87723666758	-0.300013129973	33.5103506037
10	3.70752524684	-0.633199815865	0.590317635771	3.2557360133	-0.715302572493	3.31402767802	-0.0570957419678	-0.215559561584	-0.366501358153	0.0927692653158	0.201152726812	0.627453376555	0.211298536962	-0.593173981807	-0.0931718014737	0.357706096697	-0.0389879410898	-0.0526004452751	0.377115028748	0.0234295218636	0.444994729499	10.1780117928	-13.213541641	32.3307956933
11	7.79175523845	1.7594057573	6.20460149489	3.93423619364	2.22999057462	8.83207089837	0.288792066021	-2.08189797408	0.940488968453	1.28417712943	-0.578152366058	1.00063107779	-0.213068192586	-0.912669158578	0.0992845106023	1.15477368843	0.0106213405185	0.0890432622265	1.25917276081	-0.0255830435202	1.08390597741	17.9320892949	4.57599602054	47.2904978065
12	2.74713492223	-0.910085508572	-1.53450667931	5.23649434037	0.615660910718	0.873576339483	-0.0656006184407	-0.152210451966	0.115921466972	0.189284766494	0.225262146461	0.264302345895	-0.223998309169	0.351605518032	-0.191710129964	0.722185961449	0.0167122412238	-0.0236344469524	0.573165878118	0.08608441	0.434995260675	19.630408257	0.767735749326	31.208826841
13	4.66764824911	-3.58022940937	-1.60310621714	6.88452882355	-0.752318407443	6.64017090149	0.289188980444	0.248812844475	-0.825778263789	-0.379830500635	-0.162953116102	0.222829500972	0.936216834616	-1.06276418524	-0.0160511230901	0.594608366852	0.00505251565018	-0.0873223195009	0.644126563067	0.0761793915626	0.524104837514	36.5576620375	-36.6803850337	44.6049867059
14	3.29275022651	-0.840518729646	0.724846680416	3.08858303934	-1.76038192294	2.26828370756	0.0896359984122	-0.311498475056	-0.731377342893	0.0246645150013	0.187962045694	0.370121839907	0.448011607705	-0.22252442902	-0.24461143272	0.506844035206	-0.0414496018237	-0.0426733963792	0.368763282202	0.00924964398806	0.464499586035	26.8833175385	-29.2905498767	43.1225173843
15	3.52389237891	-2.05923972521	-1.9670376591	5.37398888455	1.56956189331	4.35843445308	-0.423505063675	-0.126376093227	-0.0886733193762	0.688236022747	0.201132660045	0.340980668717	0.190188734828	0.00564553902801	0.0934014732477	0.314809618904	-0.120710409674	-0.142083022689	0.301676924656	0.051291981118	0.339046533996	34.7948837078	-23.1067397091	39.4784141963
16	2.61060332445	1.28756173134	-2.52099636382	8.11951869374	-5.03778797076	4.35639291349	0.120866638421	-0.0429603624298	-0.315766184873	-1.91410037584	-1.4189519011	-0.450925994094	1.05554011936	-0.146299673233	1.18452114283	2.54526672992	-0.470660184535	0.166910167151	1.70251571143	-0.0555542964112	1.70002268193	26.8286406277	-37.515564159	18.7499994472
17	1.46245327834	-1.65455704876	-3.47610228949	2.44635073985	4.58640553942	9.00612623953	0.157701372587	0.650744266952	-1.40458020882	-3.964746096	-0.542377888598	1.33336098824	0.906467647196	-0.541424906539	0.371617203111	1.75196440069	-0.0202244882687	-0.254585514	1.23887055201	-0.281407507874	1.02945986035	33.3547241737	-33.7279717224	13.4383546958
18	2.10883908862	-0.278742412493	-1.77311729144	5.38207352267	0.561035213395	1.87507521026	-0.131628646485	-0.0953214977191	-0.157411126783	-0.223947640168	-0.250164473851	-0.268871471376	-0.00811690577445	0.235556424881	0.232424037761	0.353469010219	-0.00724912513932	-0.0788020373328	0.464909804141	0.0188140604803	0.376245243453	39.6371550117	-23.1174519444	33.4540171826
19	5.20872326997	0.287796501688	-1.08355499454	2.00244356483	-2.86124539267	4.18417387502	0.284608908844	-0.404461372019	0.412642616391	1.27868835528	-0.685841163176	-1.94557900788	-0.77527815839	1.47488363095	0.377563055205	0.676442528481	-0.0519733352404	-0.263027108086	1.14026533516	0.265696056303	1.24554251039	62.3774575014	-12.7620893071	37.2864536254
20	0.681072181418	-0.780781165966	0.530240793604	1.44043579791	-0.580883772736	3.35803484911	0.37680834009	-0.766521990156	-0.0103954305387	-0.0507156260346	-0.134993602836	0.175266705535	-0.494738338695	0.966219840713	-0.0881535372024	0.785662450389	-0.24037091658	-0.140696057726	1.76550750964	0.535533876349	1.65175065586	67.6308131124	-10.6264844315	36.7837128208
21	1.07651398573	-1.47831059689	1.01798965361	2.12785137748	-1.5950942338	1.35760745249	-0.0735334661155	0.177858536199	0.240577513886	-1.45349710467	-0.173784498831	-0.603429318185	0.700836122145	0.533737798484	0.444360657852	0.932042470059	0.0118079545666	0.117819576912	1.79001897465	0.632832988459	1.71666993018	67.3425806554	-10.0660129697	23.0712151357
22	4.2929198405	-1.61677604557	0.002920356649	5.18857203038	0.44188229468	1.50004436937	-0.128040599669	0.386142833803	0.397175403087	-0.154523509013	-0.326650459003	-1.17140203566	-0.230573943622	0.369655640358	0.531088464628	0.591131020466	-0.134341356167	-0.0242937999777	0.787180070799	0.222967124111	0.721897195165	53.6405291338	-3.15910706358	26.7453818167
23	2.47200422543	-0.568293571222	-0.0645669428776	4.46771112375	1.51236186285	2.84948095775	-0.0397447361305	-0.204900272743	0.21252882805	-0.168786203216	-0.119833504666	-0.412512230657	-0.381515561295	0.684007532024	0.225569568552	0.507471298335	-0.0699228973614	-0.134187111615	0.653386695058	0.135499470682	0.455036942251	45.9833777526	-8.62887257899	30.5491269951
24	5.47174809593	1.4613100571	5.69652460426	8.83446773471	-1.00725108911	6.6937722188	-1.6196135459	1.26858028494	0.513513698674	1.83968584879	0.643027283194	-1.56365654042	-2.49899695483	1.44215789451	0.824711976674	1.56473732397	-0.20103939583	-0.353321333793	1.16562855286	0.165206785913	1.197130145	50.2103897124	6.8949203751	49.315088723
25	1.65675365922	0.776705503387	-2.11981377258	5.24437657043	3.18160342695	6.28251595597	-0.826824643865	-0.549009841468	0.787858377599	0.119664516444	0.526122907071	-0.517159562339	-1.27295544825	1.33370678568	0.482743706058	1.36179224985	-0.0734374528806	-0.404787724767	0.983040579614	0.101919847688	0.805735756901	44.3985852882	4.0809816577	55.1620183788
26	5.09350034014	-0.835472555521	-1.36071918675	7.05358379047	3.80684475668	8.0347985375	-0.345540398378	-0.230781055418	-0.0364010933407	0.598548708728	-0.41338716663	0.142325668167	-0.194422541644	0.481721052401	0.752177384387	0.638269836333	-0.0491072424312	-0.122803880269	0.540042940539	0.135066803514	0.509673640134	44.205151124	-13.4814062883	39.8968147361

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 6 through 45 )	A	A	6 - 45	1 - 40
2	2	chain 'A' and (resid 46 through 71 )	A	A	46 - 71	41 - 66
3	3	chain 'A' and (resid 72 through 108 )	A	A	72 - 108	67 - 103
4	4	chain 'A' and (resid 109 through 137 )	A	A	109 - 137	104 - 132
5	5	chain 'A' and (resid 138 through 195 )	A	A	138 - 195	133 - 190
6	6	chain 'A' and (resid 196 through 223 )	A	A	196 - 223	191 - 218
7	7	chain 'A' and (resid 224 through 266 )	A	A	224 - 266	219 - 261
8	8	chain 'B' and (resid 5 through 21 )	B	C	5 - 21	1 - 17
9	9	chain 'B' and (resid 22 through 58 )	B	C	22 - 58	18 - 54
10	10	chain 'B' and (resid 59 through 190 )	B	C	59 - 190	55 - 186
11	11	chain 'B' and (resid 191 through 223 )	B	C	191 - 223	187 - 201
12	12	chain 'B' and (resid 224 through 266 )	B	C	224 - 266	202 - 244
13	13	chain 'C' and (resid 5 through 45 )	C	D	5 - 45	1 - 41
14	14	chain 'C' and (resid 46 through 177 )	C	D	46 - 177	42 - 173
15	15	chain 'C' and (resid 178 through 195 )	C	D	178 - 195	174 - 191
16	16	chain 'C' and (resid 196 through 209 )	C	D	196 - 209	192 - 205
17	17	chain 'C' and (resid 210 through 224 )	C	D	210 - 224	206 - 220
18	18	chain 'C' and (resid 225 through 266 )	C	D	225 - 266	221 - 262
19	19	chain 'D' and (resid 6 through 47 )	D	E	6 - 47	1 - 42
20	20	chain 'D' and (resid 48 through 71 )	D	E	48 - 71	43 - 66
21	21	chain 'D' and (resid 72 through 85 )	D	E	72 - 85	67 - 80
22	22	chain 'D' and (resid 86 through 137 )	D	E	86 - 137	81 - 132
23	23	chain 'D' and (resid 138 through 195 )	D	E	138 - 195	133 - 190
24	24	chain 'D' and (resid 196 through 209 )	D	E	196 - 209	191 - 204
25	25	chain 'D' and (resid 210 through 223 )	D	E	210 - 223	205 - 218
26	26	chain 'D' and (resid 224 through 266 )	D	E	224 - 266	219 - 261

-
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://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