PDB-9c5l: Trypanosoma cruzi beta-3-HBDH R19T/K20S/C64Y mutant in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 9c5l

Title

Trypanosoma cruzi beta-3-HBDH R19T/K20S/C64Y mutant in complex with NADH and malonate (C2 space group)

Components

Hydroxybutyrate dehydrogenase

Keywords

OXIDOREDUCTASE / Trypanosoma cruzi / NADH / 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: 1.6 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

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Download

PDBx/mmCIF format	9c5l.cif.gz	699.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9c5l.ent.gz	490 KB	Display	PDB format
PDBx/mmJSON format	9c5l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9c5l_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	9c5l_full_validation.pdf.gz	2.9 MB	Display
Data in XML	9c5l_validation.xml.gz	56 KB	Display
Data in CIF	9c5l_validation.cif.gz	74.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/9c5l ftp://data.pdbj.org/pub/pdb/validation_reports/c5/9c5l	HTTPS FTP

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Related structure data

Related structure data	9c5hC 9c5iC 9c5jC 9c5kC 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

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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) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #77 - May 2006 Glucose Oxidase similarity (2)

Deposited unit

A: Hydroxybutyrate dehydrogenase

B: Hydroxybutyrate dehydrogenase

C: Hydroxybutyrate dehydrogenase

D: Hydroxybutyrate dehydrogenase

hetero molecules

117 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)	119.720, 80.300, 122.650
Angle α, β, γ (deg.)	90.000, 107.580, 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-542- HOH

#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-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₂O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 824 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 49.96 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.2 M Li2SO4, 0.1 M Bis-tris pH 6.5

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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: 1.6→37.97 Å / Num. obs: 145724 / % possible obs: 99.9 % / Redundancy: 6.9 % / B_iso Wilson estimate: 26.56 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.057 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 7 % / R_merge(I) obs: 1.016 / Mean I/σ(I) obs: 2 / Num. unique obs: 10779 / CC_1/2: 0.748 / % possible all: 99.9

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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: 1.6→37.97 Å / SU ML: 0.1424 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1781	2000	1.37 %	random
R_work	0.1572	143700	-	-
obs	0.1575	145700	99.91 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 36.83 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→37.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7632	0	208	835	8675

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0083	8037
X-RAY DIFFRACTION	f_angle_d	0.9482	10951
X-RAY DIFFRACTION	f_chiral_restr	0.0723	1295
X-RAY DIFFRACTION	f_plane_restr	0.0083	1391
X-RAY DIFFRACTION	f_dihedral_angle_d	13.7737	2860

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 (%)
1.6-1.64	0.2571	142	0.2451	10237	X-RAY DIFFRACTION	99.89
1.64-1.68	0.1908	141	0.2199	10158	X-RAY DIFFRACTION	99.91
1.68-1.73	0.2208	143	0.2001	10212	X-RAY DIFFRACTION	99.93
1.73-1.79	0.2003	142	0.1889	10241	X-RAY DIFFRACTION	99.93
1.79-1.85	0.1918	143	0.1958	10241	X-RAY DIFFRACTION	99.86
1.85-1.93	0.2197	142	0.1893	10220	X-RAY DIFFRACTION	99.97
1.93-2.02	0.2019	143	0.1694	10255	X-RAY DIFFRACTION	99.99
2.02-2.12	0.1993	143	0.1629	10259	X-RAY DIFFRACTION	99.94
2.12-2.25	0.173	143	0.1596	10258	X-RAY DIFFRACTION	99.95
2.25-2.43	0.159	142	0.1494	10233	X-RAY DIFFRACTION	99.9
2.43-2.67	0.1792	144	0.1545	10304	X-RAY DIFFRACTION	99.86
2.67-3.06	0.2065	142	0.1569	10282	X-RAY DIFFRACTION	99.96
3.06-3.85	0.1684	144	0.1485	10339	X-RAY DIFFRACTION	99.94
3.85-37.97	0.1545	146	0.1427	10461	X-RAY DIFFRACTION	99.78

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	3.23607246629	-0.150118966126	0.331830356195	2.67227394247	-1.24643174215	2.70470514647	-0.0083894967175	0.211159602438	0.0281556751742	-0.0369884697873	-0.0559898582018	-0.0983721990033	-0.214427934015	0.153188029434	0.06549936725	0.391721856367	-0.00689456394625	0.00720128645303	0.201715522922	0.0208799024343	0.20032414707	30.0545728687	18.953142463	11.4236976517
2	0.535226097674	-0.0943700558759	0.226947412213	1.63443382669	-0.514704199776	1.21711796671	-0.00515569777194	0.0670699841204	0.0644043748577	-0.0454878422204	-0.102241551526	-0.238082211827	-0.314649726947	0.158238065522	0.0872933562808	0.293125331155	-0.0450053238584	-0.000223646034312	0.206843278476	0.0258006186111	0.203362729194	37.0420382995	6.81301026555	21.2643135268
3	5.62514594368	-2.27143267067	-3.30590392211	3.50310933014	4.05271842823	5.78524708969	0.37085824574	-0.0108924376304	0.685617308558	-0.959544785415	0.619926582479	-0.641766111777	-0.981074735689	0.523328539634	-0.7060921013	0.559686682121	-0.103960331054	0.0977163170323	0.323630348274	-0.0545360937605	0.328367575003	37.0904354055	-5.75767373364	1.24034776918
4	0.492900822801	-0.129249193641	-0.202186291334	1.23670868234	0.047986675859	1.42574796513	0.00646492628976	0.0250685568944	-0.0478811563869	-0.148277721763	-0.00400635924509	0.0811634470119	-0.0665886143096	-0.0909346879045	-0.00974952539722	0.277563511416	0.00136740991681	-0.00459186663368	0.235532534788	-0.00882673082987	0.214705656046	25.8132395434	-3.05047598922	14.7961050627
5	3.02694626165	0.0401586644836	-0.104982782136	2.77916057581	0.925097650849	1.88392081287	-0.0471698652964	-0.371315689575	0.216010620606	0.178972427161	-0.108328380668	0.3597512157	-0.114023356675	-0.363239002952	0.0755367954017	0.180066693111	0.0828114375072	0.0142731242457	0.397592379032	-0.0183586927582	0.365733224706	1.16269773542	0.146604460925	29.8637849944
6	1.28201168345	0.519816368644	-0.333444753619	4.1238006074	-0.957459755371	1.29924703275	0.257987861967	-0.445272081921	0.315686508137	0.20142408148	-0.366376337022	0.358229757101	-0.149850345255	-0.0514070195581	0.105645564541	0.262258249966	0.0558744682847	0.0567963093143	0.594057664582	-0.0659533213662	0.435888289403	-4.13378467431	-1.66298439817	32.4112941798
7	0.947120020107	-0.557521315546	1.42604331277	0.938138079591	-0.962449158062	2.78207190599	-0.00795659577344	-0.219540042731	-0.0845759491176	-4.08226874377E-5	0.114842936186	0.251885598932	0.0493959176016	-0.391070515059	-0.128389629567	0.227416396676	0.0175977914509	0.0522240730443	0.418006333721	0.0267328608789	0.346781410747	4.87771379063	-11.765833905	34.7284587825
8	1.17893257476	-0.11978203903	0.857715788131	0.969516825998	-0.0870562590015	2.54513183108	-0.0326572368052	-0.136013411653	-0.0274311256655	0.0229669462027	0.0945474148205	0.16827997189	-0.0455076520689	-0.309235154167	-0.0497283234305	0.201606550337	0.0171481897875	0.031903580821	0.277928332587	0.00546346520179	0.264186563319	14.2980066968	-11.176770543	31.7246077812
9	3.21147182115	1.89650538412	-1.25459691375	2.19846534839	0.629216595204	2.23183978747	0.139153103374	-1.73958786313	0.60228963007	1.35462833194	-0.0432287006646	1.05602913327	-0.818939877622	-1.13318944469	-0.00998921851372	1.1490057249	0.250500920742	0.193616139214	1.11971374076	-0.0872165752649	0.562848125232	17.8592185576	4.52453962106	53.3037332726
10	1.1328467214	0.274423157399	1.38988172557	1.2916683137	0.0722536628442	2.1901155232	-0.100408193179	-0.0449295272381	0.0963159435806	0.0809453347632	0.00339401045122	0.184351306085	-0.325091885743	-0.202940420616	0.0882389441616	0.265776596205	0.0313626502663	0.0392158818076	0.234068328445	-0.00543365389941	0.222946334244	19.0095161369	2.45423726805	30.1450959734
11	4.28754090791	-1.36309245951	-0.234999783913	4.07843753177	-0.558824688435	3.75751367361	-0.0688025455769	0.193972341113	-0.491114014461	-0.231735592905	0.0096666970597	0.047899119513	0.517680004115	-0.005603012205	0.0530265471146	0.299698850505	-0.0185209974608	0.013843810029	0.196554585994	0.00891091112494	0.284156913813	35.2339611481	-37.7341807105	44.8617782518
12	0.837312212371	-0.26271252674	0.494029312383	0.694833857638	-0.447538881135	1.48353419625	0.0349102088779	-0.101129520176	-0.14894035378	0.0172145999787	0.0467596397263	0.10419961244	0.142523000432	-0.1415710751	-0.103532952308	0.23214403021	-0.0188418409556	0.0295689188134	0.240200339566	0.0106626018364	0.26029936572	25.8484088537	-23.8904262019	42.6427738856
13	6.55616944598	1.5214293757	4.02602122447	4.58299646918	2.80974633288	3.3086916358	0.183982670188	0.394842670452	-0.957152970621	-0.558632059811	-0.230865639767	0.381299836745	1.46250191363	-0.544480847436	0.270744775914	0.688874498743	-0.0628302548986	0.00421721227862	0.332551206005	-0.0884554530289	0.401327994554	32.9122167848	-31.9411073948	20.6675293865
14	0.807863311527	-0.288529115088	0.160526221057	1.20657488541	0.0285354377811	2.49054999541	0.0542309508797	0.0845066910598	-0.0996472272906	-0.0637354932562	-0.0801136181878	-0.103499262924	0.107680766145	0.163753775741	0.0325042066096	0.206632025005	-0.00583172174847	0.039969306066	0.227920121479	0.00211470582189	0.254349964496	39.1903380954	-21.5947449363	33.363529339
15	3.91291559131	1.0149506738	-1.38602569964	1.8349966339	-0.0483593474996	4.08291877706	-0.0084572646767	-0.197253591561	0.181456141156	0.306537433008	-0.294975930793	-0.660861346414	-0.224090271257	0.768536454043	0.108229419942	0.262023910416	-0.0624193000455	-0.0809508781958	0.479442208134	0.16855020454	0.552185197536	61.817206477	-12.2212391742	37.4250553365
16	1.67194937605	0.382629297834	-0.464708235065	2.15159023771	-1.34187077331	1.63969342455	-0.12972715935	0.235297663767	0.242227401967	0.0389464680658	-0.39202907004	-0.684203394376	-0.22848482259	0.787134040928	0.404117066921	0.319662269954	-0.116767780476	-0.0375945352648	0.646128973357	0.247525128399	0.711636877323	67.2365060499	-9.01800188796	31.8376444155
17	0.893072745065	-0.22619286564	0.139570987922	1.42742641964	-0.550248668377	1.29581576789	-0.0535693398677	0.00449511579278	0.0782769816331	0.167119003907	-0.130911097396	-0.389500722887	-0.243587838606	0.248285365555	0.0830189552538	0.218433816549	-0.0688121849287	-0.0383422624665	0.253489806598	0.0512413942497	0.298174219202	47.7520979935	-4.59654923117	35.0379481332

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 85 )	A	A	6 - 85	1 - 80
2	2	chain 'A' and (resid 86 through 195 )	A	A	86 - 195	81 - 190
3	3	chain 'A' and (resid 196 through 209 )	A	A	196 - 209	191 - 204
4	4	chain 'A' and (resid 210 through 266 )	A	A	210 - 266	205 - 261
5	5	chain 'B' and (resid 4 through 47 )	B	D	4 - 47	1 - 44
6	6	chain 'B' and (resid 48 through 71 )	B	D	48 - 71	45 - 68
7	7	chain 'B' and (resid 72 through 108 )	B	D	72 - 108	69 - 105
8	8	chain 'B' and (resid 109 through 195 )	B	D	109 - 195	106 - 192
9	9	chain 'B' and (resid 196 through 225 )	B	D	196 - 225	193 - 222
10	10	chain 'B' and (resid 226 through 266 )	B	D	226 - 266	223 - 263
11	11	chain 'C' and (resid 5 through 71 )	C	G	5 - 71	1 - 67
12	12	chain 'C' and (resid 72 through 190 )	C	G	72 - 190	68 - 186
13	13	chain 'C' and (resid 191 through 223 )	C	G	191 - 223	187 - 204
14	14	chain 'C' and (resid 224 through 266 )	C	G	224 - 266	205 - 247
15	15	chain 'D' and (resid 6 through 47 )	D	J	6 - 47	1 - 42
16	16	chain 'D' and (resid 48 through 85 )	D	J	48 - 85	43 - 80
17	17	chain 'D' and (resid 86 through 266 )	D	J	86 - 266	81 - 261

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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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