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- PDB-6acq: Crystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 6acq
TitleCrystal structure of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum, apo form
Components3-hydroxybutyryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase / 3-hydroxybutyryl-CoA dehydrogenase activity / butyrate metabolic process / NAD+ binding
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTakenoya, M. / Taguchi, S. / Yajima, S.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from Clostridium acetobutylicum.
Authors: Takenoya, M. / Taguchi, S. / Yajima, S.
History
DepositionJul 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)196,7586
Polymers196,7586
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18120 Å2
ΔGint-75 kcal/mol
Surface area65400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.434, 134.479, 153.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3-hydroxybutyryl-CoA dehydrogenase / / Beta-hydroxybutyryl-CoA dehydrogenase / BHBD


Mass: 32793.043 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: hbd, CA_C2708 / Production host: Escherichia coli (E. coli)
References: UniProt: P52041, 3-hydroxybutyryl-CoA dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 3.52 Å3/Da / Density % sol: 65.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.25% PEG 400, 2.2 M ammonium sulfate, 0.1 M HEPES-NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 95544 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.9
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4717 / CC1/2: 0.855 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AA8

6aa8


Resolution: 2.5→47.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.391 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22182 4780 5 %RANDOM
Rwork0.19862 ---
obs0.19979 90674 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.979 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---2.83 Å20 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12912 0 0 79 12991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913096
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212986
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.98417647
X-RAY DIFFRACTIONr_angle_other_deg0.757330136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6151697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0424.98490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.24152459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6581562
X-RAY DIFFRACTIONr_chiral_restr0.070.22081
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022409
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_it2.5655.2236806
X-RAY DIFFRACTIONr_mcbond_other2.5655.2226805
X-RAY DIFFRACTIONr_mcangle_it4.0467.8248497
X-RAY DIFFRACTIONr_mcangle_other4.0457.8258498
X-RAY DIFFRACTIONr_scbond_it2.9065.626290
X-RAY DIFFRACTIONr_scbond_other2.9055.626290
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.828.2459151
X-RAY DIFFRACTIONr_long_range_B_refined6.63863.56415045
X-RAY DIFFRACTIONr_long_range_B_other6.63863.56915044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 338 -
Rwork0.299 6389 -
obs--95.59 %

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