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- PDB-9c5j: Trypanosoma cruzi beta-3-HBDH APO structure (P43212 space group) -

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Basic information

Entry
Database: PDB / ID: 9c5j
TitleTrypanosoma cruzi beta-3-HBDH APO structure (P43212 space group)
ComponentsHydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / 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
3-hydroxybutyrate dehydrogenase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsHashimoto, H. / Debler, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI165840 United States
CitationJournal: To Be Published
Title: Trypanosoma cruzi D-3-hydroxybutyrate dehydrogenase (HBDH) is NADP-dependent enzyme.
Authors: Hashimoto, H. / Debler, E.W.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxybutyrate dehydrogenase
B: Hydroxybutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)57,2342
Polymers57,2342
Non-polymers00
Water79344
1
A: Hydroxybutyrate dehydrogenase
B: Hydroxybutyrate dehydrogenase

A: Hydroxybutyrate dehydrogenase
B: Hydroxybutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)114,4684
Polymers114,4684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11120 Å2
ΔGint-91 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.930, 71.930, 229.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Hydroxybutyrate dehydrogenase


Mass: 28617.025 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium Citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.64→46.51 Å / Num. obs: 18576 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 67.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.4
Reflection shellResolution: 2.64→2.71 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1339 / CC1/2: 0.823 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→46.51 Å / SU ML: 0.405 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 881 5.01 %Random
Rwork0.2359 16719 --
obs0.237 17600 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.83 Å2
Refinement stepCycle: LAST / Resolution: 2.69→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 0 46 3672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293684
X-RAY DIFFRACTIONf_angle_d0.49384997
X-RAY DIFFRACTIONf_chiral_restr0.0431598
X-RAY DIFFRACTIONf_plane_restr0.0035643
X-RAY DIFFRACTIONf_dihedral_angle_d10.78351306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.860.40341430.31152702X-RAY DIFFRACTION99.75
2.86-3.080.38651430.32252719X-RAY DIFFRACTION99.83
3.08-3.390.28271440.27422733X-RAY DIFFRACTION99.83
3.39-3.880.27651450.24222762X-RAY DIFFRACTION100
3.88-4.890.21781490.20712810X-RAY DIFFRACTION100
4.89-46.510.22861570.21622993X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.603296063512.02063359965-2.774584268039.67692574622-0.3428629049236.55927379321-0.1352486491111.787685193250.0727439893202-0.5426549991820.2008503607680.5182928619590.254113556703-0.965392932904-0.1344752271520.7439930686570.0298022566178-0.05300631591630.973848587732-0.1999415657420.527860925662-6.94188897549-28.5296034589-21.0338683904
23.55963496232-0.631689947906-2.197522629513.103373013121.740178857624.18594016401-0.1412847664350.729760982457-0.726660435986-0.167338076995-0.05673763469080.1831893369490.716824946968-0.5424022743770.2539841270631.04206903255-0.0981684146833-0.04035935034151.11651384171-0.2729093762940.833437321511-11.7137691467-35.1298028015-18.4738398953
32.628660173260.08171603957410.2154079861963.43083097966-0.4127259782443.790343064460.03209605323110.665441860964-0.0188938391284-0.153729542250.138794797318-0.1253081133730.144074914914-0.115947949153-0.1705486775930.448930998383-0.01905712593-0.04044749802270.677819020047-0.02954256329720.3350539823-12.1895003867-17.0267475045-11.2615267563
40.79641972044-0.189578514547-0.1005411180493.31854314495-1.767291915950.9902200028510.2615730702210.149146962731-0.843222425956-0.2451219019470.246178959993-0.6083828475890.3464320931370.675135158284-0.2237460729430.71752699178-0.002217760879660.08600079745951.46697323959-0.1268169765361.0351312579518.4109660545-9.8988710826-17.6522137947
51.85690159723.674665390073.478691410467.391258417066.702719710737.28197518607-0.03195721556920.514750462239-0.3561351181110.1568987150961.62223189693-1.423876857760.5529292839323.71533153963-1.711484058850.939212722397-0.02410040716860.02807147371882.16979224668-0.2889718701171.5282684278826.283072272-7.0505948108-14.783626846
61.472616511540.6838046427460.1040226572360.822360468683-0.3994575020910.406454581431-0.421411702770.2991711158680.704018864536-0.3533861299370.1534105685450.112104586192-0.2159040544730.191479572008-0.05649714329331.13141793067-0.7234028976680.4350074925821.94879160844-0.591626935672.2997957796721.84538847516.6270802059-19.3365349537
72.932475546520.23754816962-1.370973170832.420474508740.3378402615290.826629932920.1423901141360.1712079843480.5265965786940.03300869103480.356669581894-0.673727624484-0.8707747179961.31459987099-0.517268365250.622093436689-0.2379540198230.1197172826050.88726969486-0.09551618894680.8201140957599.646897839541.30062077036-6.82676891526
85.001616568385.36615992539-1.364993220429.36857958248-1.660589985832.767697647940.914719467983-2.35937179399-1.460024609942.56548777527-0.828661893986-2.674420239730.3265679398931.31955539911-0.02530476719831.230600765010.00415707830142-0.4579441895361.61160871733-0.1491022758821.6567482112311.3855872666-18.08818242796.2691824333
93.40250866812-0.296192839229-2.577483572614.007441745541.047759436562.76128724846-0.3429673216490.449945316669-0.1292636278260.03621479257210.598666434868-0.7395209812410.7193931921231.07522845246-0.3870751468370.565860247212-0.0808309448446-0.006057533963281.00133672891-0.2013059098130.88400660328110.9146996964-14.3676533188-12.6097054159
104.32162877559-1.72361190755-1.582222681723.691392299370.5383451509371.22204296168-0.03427111803780.5780210445180.162027844042-0.2205351134360.278683704953-0.465421303518-0.677488893707-0.054258789307-0.1682110023690.565699769062-0.0715140078824-0.09112021163730.753303325511-0.09052311903160.613450362841.95854603239-11.0330577664-9.05741590777
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 47 )AA5 - 471 - 43
22chain 'A' and (resid 48 through 85 )AA48 - 8544 - 81
33chain 'A' and (resid 86 through 266 )AA86 - 26682 - 262
44chain 'B' and (resid 5 through 46 )BB5 - 461 - 35
55chain 'B' and (resid 47 through 71 )BB47 - 7136 - 60
66chain 'B' and (resid 72 through 85 )BB72 - 8561 - 74
77chain 'B' and (resid 86 through 190 )BB86 - 19075 - 179
88chain 'B' and (resid 191 through 233 )BB191 - 233180 - 198
99chain 'B' and (resid 234 through 245 )BB234 - 245199 - 210
1010chain 'B' and (resid 246 through 266 )BB246 - 266211 - 231

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