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- PDB-9fbd: Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Ther... -

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Basic information

Entry
Database: PDB / ID: 9fbd
TitleCrystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Thermus thermophilus HB27 complexed to NAD+
Components3-hydroxybutyryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / NAD binding / butyrate metabolic process / cellular catabolic process / Fatty acid metabolism
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase / 3-hydroxybutyryl-CoA dehydrogenase activity / fatty acid beta-oxidation / NAD+ binding
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHurtado-Guerrero, R. / Macias-Leon, J. / Gines-Alcober, I. / Gonzalez-Ramirez, A.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: Protein Sci. / Year: 2025
Title: Loop engineering of enzymes to control their immobilization and ultimately fabricate more efficient heterogeneous biocatalysts.
Authors: Zeballos, N. / Gines-Alcober, I. / Macias-Leon, J. / Andres-Sanz, D. / Gonzalez-Ramirez, A.M. / Sanchez-Costa, M. / Merino, P. / Hurtado-Guerrero, R. / Lopez-Gallego, F.
History
DepositionMay 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 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: 3-hydroxybutyryl-CoA dehydrogenase
B: 3-hydroxybutyryl-CoA dehydrogenase
C: 3-hydroxybutyryl-CoA dehydrogenase
D: 3-hydroxybutyryl-CoA dehydrogenase
E: 3-hydroxybutyryl-CoA dehydrogenase
F: 3-hydroxybutyryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,90612
Polymers190,9256
Non-polymers3,9816
Water12,592699
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Hexameric structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16290 Å2
ΔGint-98 kcal/mol
Surface area74000 Å2
Unit cell
Length a, b, c (Å)87.202, 148.289, 97.442
Angle α, β, γ (deg.)90.00, 111.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 288
2010B2 - 288
1020A2 - 288
2020C2 - 288
1030A2 - 288
2030D2 - 288
1040A2 - 290
2040E2 - 290
1050A2 - 290
2050F2 - 290
1060B2 - 289
2060C2 - 289
1070B2 - 289
2070D2 - 289
1080B2 - 288
2080E2 - 288
1090B2 - 288
2090F2 - 288
10100C2 - 289
20100D2 - 289
10110C2 - 288
20110E2 - 288
10120C2 - 288
20120F2 - 288
10130D2 - 288
20130E2 - 288
10140D2 - 288
20140F2 - 288
10150E2 - 290
20150F2 - 290

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
3-hydroxybutyryl-CoA dehydrogenase


Mass: 31820.857 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: MEVKRIGVVGAGQMGSGIAQVAASAGYEVVLVDVAESFLERGLAAIRRSLGKFLEKGKIT QEAHDEALGRIRTSLSLEDLKDADLIVEAIVEDEGEKRRLFERLGALAKPEAILASNTSS IPITALARYSGRPERFIGMHFFNPVPLMQLVEVIRGELTSEATRDVVVEVARRMGKTPLE ...Details: MEVKRIGVVGAGQMGSGIAQVAASAGYEVVLVDVAESFLERGLAAIRRSLGKFLEKGKIT QEAHDEALGRIRTSLSLEDLKDADLIVEAIVEDEGEKRRLFERLGALAKPEAILASNTSS IPITALARYSGRPERFIGMHFFNPVPLMQLVEVIRGELTSEATRDVVVEVARRMGKTPLE VQDYPGFISNRLLMPMINEAIEALREGVATKEAIDGIMRLGMNHPMGPLELADFIGLDTC LAIMEVLHRGFGDDKYRPSPLLRRMVQAGLLGRKAGRGFYTYDEKGNKVG
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C0898 / Production host: Escherichia coli (E. coli)
References: UniProt: Q72J81, 3-hydroxybutyryl-CoA dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: LiNaK Buffer System 5 pH = 7.5 Precipitant Mix 5, both the Buffer System 5 and the Precipitant Mix 5 are available at Molecular Dimensions website

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 212528 / % possible obs: 99.8 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 30901 / CC1/2: 0.459 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.93 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.711 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22601 8537 4 %RANDOM
Rwork0.19959 ---
obs0.20066 203949 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.143 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å21.7 Å2
2---3.39 Å2-0 Å2
3---3.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13301 0 264 699 14264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313791
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713623
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.64718604
X-RAY DIFFRACTIONr_angle_other_deg1.3331.57931296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15951727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52320.216740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.239152487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.68915151
X-RAY DIFFRACTIONr_chiral_restr0.0770.21789
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023093
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1885.1546922
X-RAY DIFFRACTIONr_mcbond_other4.1875.1546920
X-RAY DIFFRACTIONr_mcangle_it5.4417.7138640
X-RAY DIFFRACTIONr_mcangle_other5.4417.7138640
X-RAY DIFFRACTIONr_scbond_it5.3775.786869
X-RAY DIFFRACTIONr_scbond_other5.3775.7816870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9318.4259964
X-RAY DIFFRACTIONr_long_range_B_refined9.41460.8314917
X-RAY DIFFRACTIONr_long_range_B_other9.41960.70214819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A91400.06
12B91400.06
21A91390.06
22C91390.06
31A91860.05
32D91860.05
41A91570.06
42E91570.06
51A91460.06
52F91460.06
61B91590.06
62C91590.06
71B91670.06
72D91670.06
81B91370.07
82E91370.07
91B90770.07
92F90770.07
101C91740.05
102D91740.05
111C91470.06
112E91470.06
121C91060.06
122F91060.06
131D91980.05
132E91980.05
141D91460.05
142F91460.05
151E92130.06
152F92130.06
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 637 -
Rwork0.385 15025 -
obs--99.5 %

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