PDB-9c5n: Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH APO structure

ID or keywords:

Entry

Database: PDB / ID: 9c5n

Title

Trypanosoma cruzi R19T/K20S/C64Y mutant beta-3-HBDH APO 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	9c5n.cif.gz	645.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9c5n.ent.gz	491.3 KB	Display	PDB format
PDBx/mmJSON format	9c5n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9c5n_validation.pdf.gz	459 KB	Display	wwPDB validaton report
Full document	9c5n_full_validation.pdf.gz	467.1 KB	Display
Data in XML	9c5n_validation.xml.gz	53.7 KB	Display
Data in CIF	9c5n_validation.cif.gz	73.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/9c5n ftp://data.pdbj.org/pub/pdb/validation_reports/c5/9c5n	HTTPS FTP

-
Related structure data

Related structure data	9c5hC 9c5iC 9c5jC 9c5kC 9c5lC 9c5mC 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)	119.530, 80.270, 122.520
Angle α, β, γ (deg.)	90.000, 107.090, 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: 28578.861 Da / Num. of mol.: 4 / Mutation: R19T, K20S, C64Y 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: pED714 Details (production host): His-3C-TcHBDH R19T/K20S/C64Y 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.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 805 / 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: 2.46 Å³/Da / Density % sol: 49.95 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammmonium Tartrate, 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: 1.033167 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2023
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033167 Å / Relative weight: 1
Reflection	Resolution: 1.69→39.04 Å / Num. obs: 123762 / % possible obs: 99.9 % / Redundancy: 6.8 % / B_iso Wilson estimate: 28.31 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.051 / Net I/σ(I): 18
Reflection shell	Resolution: 1.69→1.73 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.895 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9172 / CC_1/2: 0.77 / % possible all: 99.9

-
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→39.04 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.176	2000	1.62 %	Random
R_work	0.1509	121739	-	-
obs	0.1513	123739	99.89 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 39.64 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→39.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7737	0	28	809	8574

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0076	7931
X-RAY DIFFRACTION	f_angle_d	0.9142	10759
X-RAY DIFFRACTION	f_chiral_restr	0.0562	1272
X-RAY DIFFRACTION	f_plane_restr	0.0101	1388
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7025	2854

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	0.2666	143	0.2447	8701	X-RAY DIFFRACTION	99.82
1.73-1.78	0.2492	142	0.2135	8635	X-RAY DIFFRACTION	99.89
1.78-1.83	0.2205	142	0.1907	8660	X-RAY DIFFRACTION	99.86
1.83-1.89	0.2069	142	0.1861	8674	X-RAY DIFFRACTION	99.8
1.89-1.96	0.2139	142	0.1802	8641	X-RAY DIFFRACTION	99.93
1.96-2.04	0.1689	143	0.1563	8677	X-RAY DIFFRACTION	99.99
2.04-2.13	0.2021	142	0.1488	8657	X-RAY DIFFRACTION	99.99
2.13-2.24	0.1665	143	0.1403	8702	X-RAY DIFFRACTION	99.97
2.24-2.38	0.1891	142	0.1382	8670	X-RAY DIFFRACTION	99.91
2.38-2.57	0.1522	144	0.1408	8702	X-RAY DIFFRACTION	99.81
2.57-2.82	0.1665	142	0.1469	8665	X-RAY DIFFRACTION	99.95
2.82-3.23	0.1834	144	0.1539	8751	X-RAY DIFFRACTION	100
3.23-4.07	0.1597	143	0.1426	8755	X-RAY DIFFRACTION	99.99
4.07-39.04	0.1703	146	0.1459	8849	X-RAY DIFFRACTION	99.59

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	1.21669084447	0.261143116276	0.276372715575	0.964644582766	0.180303944855	0.457527044448	-0.0275386437154	0.156707664596	0.0376061395944	-0.0581995891275	0.0375121881609	-0.259685047289	-0.0319615808461	0.290222857616	-0.0130226173535	0.224601689896	-0.0292603320874	0.016320760962	0.356131421687	0.0267582625932	0.314683215878	35.0953657873	-37.1645666642	26.1508624858
2	1.85552073778	-0.24953760075	0.860273010184	1.95681346008	-0.350177453149	1.49153038298	-0.0334224463211	0.428043420901	0.141006011819	-0.438912220685	-0.0822853169933	-0.1508967294	-0.2033337536	0.345580594003	0.151811762664	0.362236714791	-0.0333085653901	0.03372046007	0.322441487155	0.0385280842819	0.234836764423	23.5265034982	-27.1956365699	20.6262384914
3	5.97599117633	-0.18083181616	-1.33060463129	5.03170673235	1.06386485153	6.39296040104	0.0282485951656	-0.334567530661	0.129384757864	0.188153507975	-0.0139257551966	0.120828389145	-0.166121090201	-0.045707395006	-0.0253361544118	0.306995657067	-0.00763229609946	-0.0242520863355	0.131822058437	-0.0354380554443	0.184718783027	14.5863864589	-13.1223081778	47.043528135
4	8.35574394882	-0.336055470826	0.705219253662	3.02154584975	0.902285977644	3.61285261143	0.19952463051	-0.266853916916	-0.138759948425	0.123578150488	-0.105289382995	0.179184373817	-0.155750662707	-0.17906262604	-0.0672708932598	0.383156085306	0.0257610445952	-0.00611230032618	0.211631926726	-0.0420708365432	0.250988489562	11.5462625081	-9.46700356392	50.6387245405
5	8.24137940264	7.0457602212	0.121335026422	8.68032095373	0.665283177194	4.71642304033	-0.293562442416	0.0334150159697	0.699300727564	-0.804525758425	-0.19395564085	0.955805438755	-0.990732286797	-0.711762093856	0.491945261393	0.556057912927	0.19226238578	-0.08641207143	0.349081019034	-0.0986669969305	0.398919529194	3.49936772691	-4.11308475401	41.4388714136
6	0.994351806291	0.544387833721	-0.533387794021	1.36613201183	-0.369433513932	1.1422339598	-0.0365553179423	-0.0924032372261	0.00992923984686	0.139842053026	-0.114507411125	0.148631508291	-0.202683248675	-0.131984905834	0.138803932224	0.37762999215	0.0314764512187	0.00623752355197	0.282010691281	-0.0443353338842	0.286737467955	1.87954883277	-23.6204336653	43.4085311363
7	8.33522387326	6.61155768913	-7.28783658648	8.67252376397	-6.99466233375	8.28483937352	0.0367447672827	0.109819751041	0.169865549855	0.195064843356	-0.0953073105572	0.250855606162	-0.573429103492	-0.264529358055	0.00597079767344	0.345106251078	0.0881733831903	-0.0762863431436	0.220753107723	-0.0852031486434	0.236167594708	0.242562514165	-16.6336294576	36.5118358943
8	0.782245186422	0.590569966154	-0.0892296295568	2.67053641112	-0.370422460527	2.24474591915	-0.0354470963074	-0.0303744877293	0.0567036353096	-0.0147397791906	-0.037102806423	0.138690398884	-0.202012718231	-0.0663267807894	0.0662815395541	0.277233725625	0.0334796823755	-0.0080328968303	0.211513150672	-0.00970727438157	0.236929317589	8.18679732785	-25.444060449	35.3304088621
9	6.92993480709	5.65991225997	-5.0514459913	6.29900577392	-5.86970255198	5.4971558362	0.306809817367	-0.259142907749	0.587712583358	0.544884776356	0.583049197301	0.946021237744	-0.626814396603	-0.545537125104	-0.872748107425	0.480654714665	0.0711119556731	0.0611968863163	0.377548679925	0.0812484536086	0.400403965148	5.17072508143	-34.9310806394	57.4351952974
10	0.598117209253	0.231141022407	-0.497221445602	1.48019465839	-0.648532792546	2.50718383667	0.00862614917449	-0.0234134528553	-0.0395397449201	0.126254434677	-0.018249362781	-0.0249919633964	-0.140003671468	0.0718244538276	0.0202463146314	0.253823468815	0.0046769757415	-0.0132352359372	0.228042243639	0.014414481277	0.224842582784	15.8805874073	-32.3216932873	43.6801393229
11	5.41968241205	0.514778630293	-1.65811662714	2.75506163036	-1.38801889881	4.23642815465	0.0223101757668	0.354403966384	0.148112877198	-0.256764236956	-0.287458274779	0.544280126981	-0.343620126097	-0.874168006462	0.0886834749417	0.214044908215	0.0854385469111	-0.0931908187125	0.49764755862	-0.1541607428	0.500214996862	-19.9679735295	-41.6684856621	21.7340257146
12	4.07903297442	0.705602613971	-0.195556558271	1.38529604969	1.95867348686	3.54142416046	-0.0649926631289	-0.00720967162819	0.263266505495	-0.233737069223	-0.467371912868	0.804945957993	-0.555120011678	-0.938593359774	0.216170686163	0.343486547652	0.188358536167	-0.0578489208978	0.728070956184	-0.231825054766	0.755293318259	-25.8997508523	-37.8078302526	26.327208248
13	1.04027321984	0.453644994988	0.132389276738	1.50093315951	0.0188155040061	1.1118061019	-0.0808773657665	-0.017008002371	0.0919075073077	-0.00745725977902	-0.113769205868	0.409738565177	-0.186956524384	-0.273022396919	0.145651203831	0.227793519896	0.0580811003111	-0.0169920007186	0.298539335332	-0.0653941225803	0.365628359056	-7.97097742132	-33.9397897622	29.7417294084
14	5.13212340843	3.44909683819	-2.24612345629	3.45273308011	-4.4042238511	8.75631087832	-0.288880265451	-0.174152070507	0.833955849726	-0.266846681074	0.328073284167	1.13827838659	-1.34698904279	-1.26522995106	-0.165595996106	0.779391371537	0.177606844632	-0.227793178438	0.594405138609	-0.105684801053	1.03511156532	-8.16536450081	-21.0375898699	9.55848242797
15	1.75786832765	0.63784354791	-0.114133131573	1.89525132776	-0.00681634770843	2.03760300232	-0.109348358287	0.136645701931	0.0633912790069	-0.319057467367	-0.0412379406494	0.320123894293	-0.271862850481	-0.183526785109	0.0426872034183	0.283016668069	0.0603465688845	-0.0748224646751	0.259697037628	-0.051521019969	0.294483147925	-2.41954917218	-37.1096226402	14.7534626322
16	3.74071139849	1.0308482841	-0.251775492862	6.29519005664	0.343046653292	5.88608122224	-0.0579931519796	-0.11056363505	-0.261783385173	0.201589529206	-0.0553430469649	-0.0288345130527	0.507004032475	0.0909423710452	0.0179675677164	0.247874430235	0.00528263135222	0.0406467403845	0.182737587931	-0.0170035141251	0.270475501524	5.42146431212	-65.0648109281	14.1847415512
17	9.00050477982	1.5587702359	-1.20869885188	3.79216998217	-0.0732205615746	4.49034581964	-0.173365442672	-0.0315753647252	-0.365196794388	-0.127043035824	0.0515033614595	-0.270878806203	0.37404137009	0.361543208796	0.143009081203	0.294728010635	0.0686706132657	0.0189583878534	0.209858256829	-0.0679441255435	0.319924738321	11.4160155027	-67.4593887694	8.92671709741
18	1.02050878811	0.133288260357	0.0802739321373	0.792304186928	0.456029486877	1.04495198152	-0.0145380837694	-0.037392895267	-0.154508771061	0.0966462571552	-0.0143267784011	0.00912496567003	0.160205303797	0.0376793839627	0.0315389800799	0.234926776092	0.0156198325402	0.0119773546928	0.214593684208	0.014709735621	0.267582042916	11.5395529664	-53.5153117239	23.0369867087

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 3 through 177 )	A	A	3 - 177	1 - 175
2	2	chain 'A' and (resid 178 through 266 )	A	A	178 - 266	176 - 264
3	3	chain 'B' and (resid 5 through 47 )	B	D	5 - 47	1 - 43
4	4	chain 'B' and (resid 48 through 71 )	B	D	48 - 71	44 - 67
5	5	chain 'B' and (resid 72 through 85 )	B	D	72 - 85	68 - 81
6	6	chain 'B' and (resid 86 through 108 )	B	D	86 - 108	82 - 104
7	7	chain 'B' and (resid 109 through 137 )	B	D	109 - 137	105 - 133
8	8	chain 'B' and (resid 138 through 195 )	B	D	138 - 195	134 - 191
9	9	chain 'B' and (resid 196 through 209 )	B	D	196 - 209	192 - 205
10	10	chain 'B' and (resid 210 through 266 )	B	D	210 - 266	206 - 262
11	11	chain 'C' and (resid 6 through 45 )	C	H	6 - 45	1 - 40
12	12	chain 'C' and (resid 46 through 85 )	C	H	46 - 85	41 - 80
13	13	chain 'C' and (resid 86 through 195 )	C	H	86 - 195	81 - 190
14	14	chain 'C' and (resid 196 through 209 )	C	H	196 - 209	191 - 204
15	15	chain 'C' and (resid 210 through 266 )	C	H	210 - 266	205 - 261
16	16	chain 'D' and (resid 5 through 47 )	D	J	5 - 47	1 - 43
17	17	chain 'D' and (resid 48 through 85 )	D	J	48 - 85	44 - 81
18	18	chain 'D' and (resid 86 through 266 )	D	J	86 - 266	82 - 258

-
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