PDB-9c5o: Trypanosoma cruzi R42F mutant beta-3-HBDH structure

ID or keywords:

Entry

Database: PDB / ID: 9c5o

Title

Trypanosoma cruzi R42F mutant beta-3-HBDH structure

Components

Hydroxybutyrate dehydrogenase

Keywords

OXIDOREDUCTASE / Trypanosoma cruzi / 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: 1.69 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	9c5o.cif.gz	683.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9c5o.ent.gz	479.7 KB	Display	PDB format
PDBx/mmJSON format	9c5o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9c5o_validation.pdf.gz	464.1 KB	Display	wwPDB validaton report
Full document	9c5o_full_validation.pdf.gz	474.1 KB	Display
Data in XML	9c5o_validation.xml.gz	51.7 KB	Display
Data in CIF	9c5o_validation.cif.gz	69 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/9c5o ftp://data.pdbj.org/pub/pdb/validation_reports/c5/9c5o	HTTPS FTP

-
Related structure data

Related structure data	9c5hC 9c5iC 9c5jC 9c5kC 9c5lC 9c5mC 9c5nC 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)	118.290, 80.900, 121.740
Angle α, β, γ (deg.)	90.000, 107.500, 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

Components on special symmetry positions

ID	Model	Components
1	1	C-315- HOH

#1: Protein	Hydroxybutyrate dehydrogenase Mass: 28607.002 Da / Num. of mol.: 4 / Mutation: R42F 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: pED690 / Details (production host): His-3C-TcHBDH R42F mutant / 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.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.43 Å³/Da / Density % sol: 49.33 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium fluoride, 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2022
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03317 Å / Relative weight: 1
Reflection	Resolution: 1.69→38.7 Å / Num. obs: 105256 / % possible obs: 85.9 % / Redundancy: 6.8 % / B_iso Wilson estimate: 27.52 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.052 / Net I/σ(I): 20.6
Reflection shell	Resolution: 1.69→1.73 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.724 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6706 / CC_1/2: 0.862 / % possible all: 74.4

-
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: 1.69→38.7 Å / SU ML: 0.2041 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1803	2000	1.9 %	Random
R_work	0.1597	103230	-	-
obs	0.16	105230	85.96 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 37.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→38.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7625	0	12	638	8275

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0093	7792
X-RAY DIFFRACTION	f_angle_d	0.9616	10572
X-RAY DIFFRACTION	f_chiral_restr	0.0635	1257
X-RAY DIFFRACTION	f_plane_restr	0.0124	1361
X-RAY DIFFRACTION	f_dihedral_angle_d	14.1775	2800

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 (%)
1.69-1.73	0.3099	121	0.2811	6259	X-RAY DIFFRACTION	73.49
1.73-1.78	0.2311	165	0.2203	8507	X-RAY DIFFRACTION	99.42
1.78-1.83	0.2073	164	0.1902	8453	X-RAY DIFFRACTION	98.8
1.83-1.88	0.2219	118	0.1896	6110	X-RAY DIFFRACTION	94.54
1.9-1.96	0.2087	58	0.1806	2961	X-RAY DIFFRACTION	39.04
1.96-2.04	0.1988	166	0.1707	8565	X-RAY DIFFRACTION	99.91
2.04-2.13	0.1905	99	0.1763	5124	X-RAY DIFFRACTION	59.97
2.13-2.24	0.1904	166	0.165	8566	X-RAY DIFFRACTION	99.77
2.24-2.38	0.1772	149	0.1514	7697	X-RAY DIFFRACTION	89.93
2.38-2.57	0.1638	164	0.1508	8522	X-RAY DIFFRACTION	99.19
2.57-2.82	0.1713	147	0.1596	7527	X-RAY DIFFRACTION	88.06
2.82-3.23	0.1899	167	0.1592	8614	X-RAY DIFFRACTION	100
3.23-4.07	0.153	148	0.1508	7659	X-RAY DIFFRACTION	88.66
4.07-38.7	0.1833	168	0.1511	8666	X-RAY DIFFRACTION	98.89

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	6.12893171471	0.627018687254	-0.303304341811	5.08564135946	-0.467056591061	6.09912563776	-0.00885314549559	0.483594772157	0.0902544987783	-0.420649432184	-0.00883157629353	-0.249828306641	-0.105473114659	0.160748596474	-0.0425121194119	0.340758921156	0.0308598674482	0.0196690732742	0.162200762694	0.0616151370908	0.187797189873	26.6187572461	29.052852369	11.3158214437
2	5.98698375075	-1.01149041053	2.57671570705	2.93993383901	-1.81204383598	4.48756576724	-0.00574434245413	0.252539446005	0.15098442153	-0.110374380519	-0.218476247165	-0.482414923241	-0.250458851723	0.421950412815	0.250488521049	0.391636554611	-0.0168681844416	0.0578932458643	0.256288825834	0.10599984305	0.348538054709	32.8267996907	34.6812958731	11.4740260257
3	0.890068803907	-0.087272020671	0.00854176102252	1.20554580628	-0.20652697158	1.16080578116	0.0325799487357	0.0950838508014	0.110622837458	-0.0841024369061	-0.0919291859212	-0.19138707516	-0.145549835115	0.0638085210506	0.0415400735036	0.287080528057	-0.00350588442406	0.014640556533	0.188650274529	0.027255466118	0.225967953953	36.3528527854	19.4579096243	20.9967015431
4	3.48727160704	-2.27688581421	-3.11401683854	1.7753056293	2.98501106686	7.86623379368	0.177502771723	-0.0187985059918	0.284458348467	-0.119533646942	0.145726180226	-0.12026383029	-0.263647901377	0.156028381572	-0.335679542056	0.400921889519	-0.00956999716185	0.0342432399711	0.257433480476	-0.0742808415307	0.270646597962	33.1432084761	3.2710874647	1.82998307719
5	1.14822928058	-0.720177234236	0.0226341764595	4.73637371586	1.61103330935	2.47566507366	0.0258001888126	0.0548327949566	0.0424051739599	-0.120820866651	-0.0495105172317	0.081487562535	0.043146321929	-0.0791776682848	0.013964401824	0.236354805129	0.00143149811414	0.017899517285	0.204385044662	0.00679400165536	0.172941128959	22.8613218486	13.7110038716	19.6074573645
6	5.61898588688	0.237361568855	-0.825931448205	4.56035761959	-0.20914865509	3.20784737039	0.0137601770582	-0.378347295255	0.233274903807	0.194857196912	-0.04901082953	0.538818933694	0.00673676520449	-0.193437715323	-0.0317614629529	0.170544174671	0.0475535234451	-0.0136109246973	0.256160959552	-0.0446693179151	0.316527957052	0.59440716645	13.1881843235	29.563216253
7	3.55336005566	-0.778194414318	-0.896438315248	7.66860864974	-3.45499650753	3.7819125729	0.287704747041	-0.589289673561	0.214298672567	0.85328338519	-0.103965949184	0.903499148153	-0.438981148692	-0.116276955511	-0.185326229832	0.277180309258	0.0025766530181	0.0345856169498	0.459967481237	-0.10218023772	0.42922365214	-4.55547419339	10.9922442106	32.459876517
8	6.46714831299	-5.77140456918	5.71737998807	5.32949622269	-5.22019248626	5.12347464429	0.581236287303	-0.0853233077736	-0.705654643396	-0.534964905029	-0.0292793937443	0.985817963869	0.792065299654	-0.35978308911	-0.522211254342	0.311006166415	-0.0386121949689	-0.0279313661412	0.380932011417	0.00388365185951	0.471895005077	-4.57555892833	-1.34251884443	27.7163117547
9	1.28792208905	-0.252722857235	0.465383703616	1.10643211602	-0.2318208186	1.23599549211	-0.0135226389668	-0.147604186671	-0.0288163875351	0.0129194958139	0.0314768202347	0.126779644254	-0.0158004240766	-0.202438390439	-0.039675138176	0.219496607108	0.00888764078131	-0.00230431274222	0.239247416404	-0.00900048285471	0.214765696639	13.0525061564	1.79410779394	33.1610196783
10	1.85192090995	-0.279174239543	-0.453055598497	5.88915211824	2.03237573485	2.23636823718	0.00487504658032	-1.02814043235	0.259295054589	1.19970712373	-0.125027154727	0.71156902349	-0.0313128622003	-0.233869652109	0.151490037794	0.630289620565	0.0240463342887	0.127334573894	0.569692219813	-0.103270579373	0.408901858191	17.148689937	20.9540998787	49.0827201218
11	2.71108347686	0.0718362858379	1.70573831383	1.96829099881	-0.0100151772669	2.86504246632	-0.0234403028838	-0.010037665717	0.0670282013881	-0.00367905397972	0.0176491740009	0.0655911395552	-0.127803456493	-0.0613832075124	0.0107451443397	0.248763548923	0.0180733900272	0.011760345267	0.191516633336	0.00669524788474	0.19758843363	17.9080047508	13.7068320518	27.0660344139
12	7.0545409772	-1.88169342357	-0.956108720287	8.58606116889	-0.994639756199	7.78787231332	-0.461701892392	-0.133974642343	-0.368568319492	-0.245914010785	0.297564262925	-0.447198604065	0.337546957522	-0.0350123111921	0.0316121419535	0.306274960762	0.00323587928516	0.0515827822116	0.160806859103	0.0720901684986	0.266668586776	37.4412971939	-20.4163996362	46.2207866212
13	3.55003820058	-0.449403184064	-0.403284754329	7.6191379924	-1.50898462123	4.46997103661	-0.132845142805	0.0345218423505	-0.210939179792	-0.326148831939	-0.0222364537448	-0.0325650743496	0.355486100553	0.0641583169901	0.154925114898	0.314856707138	0.0151653352937	0.0600533591986	0.23113374223	0.0362811634121	0.307391340973	36.7540840086	-22.930928042	42.5681195892
14	6.43177682736	5.33229941359	0.69984365717	4.80164569614	2.0974153312	7.04281711577	0.293586275063	0.520403682904	-1.15000907782	-0.525839212885	0.156170587821	0.979145085924	1.4221372777	-0.0395479065561	-0.31025585025	0.608998426941	-0.00403058613371	-0.0500456400538	0.30379825091	0.0450316184479	0.884905015904	36.1841142486	-32.8236148831	41.683571887
15	6.88211947913	-0.31714331075	0.244893712701	3.211475329	-1.09901212428	3.8484475648	-0.0940994975507	-0.623708225143	-0.500442975322	0.203137138615	0.12689958373	0.330634688135	0.227297305182	-0.252024797196	-0.0834040042386	0.338874410202	-0.0261821311458	0.0354264055156	0.307683426747	0.114418427095	0.395321370833	26.29460146	-23.194378291	51.9750142509
16	1.62255495953	-0.0474098408235	1.29312518047	0.741942313053	-0.227955186369	2.64828113981	0.0909564571297	-0.116624291433	-0.159365930429	-0.0450745034896	-0.00608950373384	0.0742657508383	0.253885880598	-0.117731573658	-0.10423597521	0.249887074267	-0.0105235433801	-0.0134000830655	0.212699404522	0.00257782676242	0.220271056889	24.0068003065	-10.1898497149	39.7064658742
17	3.41849901886	-0.514121963716	-0.27338834685	2.64676508474	-1.37557306982	0.767145571094	-0.103122609254	0.195224734274	-0.358889508954	-0.271289273375	-0.244134548572	0.257136258128	0.731453672408	-0.463065064751	0.245106005752	0.334216331938	-0.0648636053763	0.0375976613447	0.196006394377	-0.00283883685924	0.258887435322	31.6764194454	-12.9980202341	34.3493101615
18	2.14259002091	-0.583582418339	0.142450029261	3.0903233088	0.377057786533	6.67162633594	0.0460946448478	0.160673839744	-0.20085189789	-0.350191237994	-0.12429762854	-0.0752096250449	0.195300618333	0.0316896538625	0.0395304677465	0.180084404132	-0.00702396068142	0.0446676146299	0.16160852498	0.00275059493683	0.234320537117	37.3383463519	-10.5915685053	29.4551735124
19	8.23488067637	2.77642519846	-0.414065948146	7.33621445713	0.199741771856	4.45027980237	0.244529008228	-0.359520833788	0.146740863821	0.501880395669	-1.03698206556	-0.487698306409	0.028881415949	0.404981978417	0.609795226969	0.209712299541	0.0259687467077	-0.048692407573	0.406791445276	0.194167242875	0.535117612292	59.8226678523	-3.96101830378	34.4496233602
20	2.20447384151	-0.30172509533	-1.4757840951	0.0761542265919	0.489178168232	5.00398232445	0.0199280987885	-0.434685826477	0.525014556559	0.254383173433	-0.309363568562	-0.865426258779	-0.632279372941	0.738610679682	0.18878367792	0.265029338249	-0.0599046470497	-0.0789588094534	0.443133476889	0.12368366849	0.685302094823	61.6301626948	2.22032643317	37.1675963969
21	2.78011341563	-1.13950173708	0.988775234624	4.53280938902	-4.88536740666	5.40426074281	-0.129666656032	-0.330938135501	0.310048490024	0.814827616892	-0.637195583516	-1.30478385738	-0.813534556122	0.77725888917	0.617484244651	0.437339542093	-0.10626867778	-0.203140642694	0.614263631996	0.240830137002	0.954133018465	67.206231977	3.50972139511	36.5162615701
22	4.01500246092	-2.95045144669	-0.0107227371406	5.30394384518	-0.128829883274	1.95730956823	0.141729592193	0.529550241881	0.0922517194169	-0.634143066973	-0.492143615796	-0.808740301702	0.0369035049981	0.423131246496	0.159177915456	0.310358362525	-0.0315404267823	0.105270368742	0.612972725417	0.251186849649	0.863584972686	66.4935984236	3.8833973064	22.4904652003
23	2.70800560558	-1.77242728285	-0.639031629228	2.56482207199	-0.0833992582309	0.998117366829	-0.142662455759	-0.290038419649	0.220230574498	0.11161508791	0.164791309221	-0.808104619974	-0.0952142040399	0.287503283518	0.0348512902236	0.22857968208	-0.0570076429713	-0.0575870280168	0.300209093517	0.0613409924278	0.443905548912	51.7061038479	13.1468219836	31.7835381907
24	1.21575448462	-0.487230511007	-0.222661902036	3.15115657511	0.539787787117	1.71052843797	-0.000881936945755	0.00351985462267	0.0558281433591	-0.0871852009025	-0.133404978693	-0.50149251616	-0.0482871007492	0.211314017627	0.0920873970975	0.190422070524	-0.00850387655537	-0.000591319590724	0.234955203779	0.059322438554	0.321979517382	48.18849465	6.50067389927	27.4893346628
25	4.36285706401	1.32914212566	-1.00632221575	8.52400901506	3.63526351813	2.58443848863	-0.185712854884	0.159855411139	0.725944555294	1.06476204384	0.141739015469	-1.23603178144	-0.696442418739	0.878790582783	0.0979561463175	0.848510609801	-0.11671241828	-0.24965827195	0.521957847479	0.0671656730314	0.552255223292	46.1041528102	19.6144496693	51.7295102265
26	1.80379518953	-0.27955872801	-0.0144360186096	2.36877346082	1.02231053985	4.81326982267	-0.0259863429239	-0.0851954720636	-0.0722276767528	0.188262627967	-0.109402387756	-0.23940060109	0.0344045501392	0.121551665604	0.121006529141	0.20664669676	-0.0368432749449	-0.0379659073005	0.21087596469	0.0537988392167	0.279598496176	43.2997286141	0.241446545825	39.53658278

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 4 through 47 )	A	A	4 - 47	1 - 44
2	2	chain 'A' and (resid 48 through 85 )	A	A	48 - 85	45 - 82
3	3	chain 'A' and (resid 86 through 195 )	A	A	86 - 195	83 - 192
4	4	chain 'A' and (resid 196 through 225 )	A	A	196 - 225	193 - 222
5	5	chain 'A' and (resid 226 through 266 )	A	A	226 - 266	223 - 263
6	6	chain 'B' and (resid 3 through 47 )	B	B	3 - 47	1 - 45
7	7	chain 'B' and (resid 48 through 71 )	B	B	48 - 71	46 - 69
8	8	chain 'B' and (resid 72 through 85 )	B	B	72 - 85	70 - 83
9	9	chain 'B' and (resid 86 through 195 )	B	B	86 - 195	84 - 193
10	10	chain 'B' and (resid 196 through 233 )	B	B	196 - 233	194 - 227
11	11	chain 'B' and (resid 234 through 266 )	B	B	234 - 266	228 - 260
12	12	chain 'C' and (resid 5 through 20 )	C	F	5 - 20	1 - 16
13	13	chain 'C' and (resid 21 through 45 )	C	F	21 - 45	17 - 38
14	14	chain 'C' and (resid 46 through 58 )	C	F	46 - 58	39 - 51
15	15	chain 'C' and (resid 59 through 86 )	C	F	59 - 86	52 - 79
16	16	chain 'C' and (resid 87 through 177 )	C	F	87 - 177	80 - 170
17	17	chain 'C' and (resid 178 through 201 )	C	F	178 - 201	171 - 194
18	18	chain 'C' and (resid 202 through 266 )	C	F	202 - 266	195 - 246
19	19	chain 'D' and (resid 5 through 20 )	D	G	5 - 20	1 - 16
20	20	chain 'D' and (resid 21 through 45 )	D	G	21 - 45	17 - 41
21	21	chain 'D' and (resid 46 through 71 )	D	G	46 - 71	42 - 67
22	22	chain 'D' and (resid 72 through 85 )	D	G	72 - 85	68 - 81
23	23	chain 'D' and (resid 86 through 108 )	D	G	86 - 108	82 - 104
24	24	chain 'D' and (resid 109 through 195 )	D	G	109 - 195	105 - 191
25	25	chain 'D' and (resid 196 through 223 )	D	G	196 - 223	192 - 219
26	26	chain 'D' and (resid 224 through 266 )	D	G	224 - 266	220 - 262

-
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