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- PDB-6aa8: Crystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 6aa8
TitleCrystal structure of (S)-3-hydroxybutyryl-coenzymeA dehydrogenase from Clostridium acetobutylicum complexed with NAD+
Components3-hydroxybutyryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Complex / Rossmann fold
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydrogenase / butyrate metabolic process / 3-hydroxybutyryl-CoA dehydrogenase activity / fatty acid beta-oxidation / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxybutyryl-CoA dehydrogenase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,0858
Polymers196,7586
Non-polymers1,3272
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20210 Å2
ΔGint-104 kcal/mol
Surface area63860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.375, 157.939, 81.797
Angle α, β, γ (deg.)90.00, 100.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-hydroxybutyryl-CoA dehydrogenase / (S)-3-hydroxybutyl-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 (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 17.5% PEG 3350, 200mM sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 109647 / % possible obs: 98.6 % / Redundancy: 2.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.316 / Num. unique obs: 5492 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R1N

4r1n


Resolution: 2.1→48.46 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.701 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 5496 5 %RANDOM
Rwork0.19244 ---
obs0.19402 104116 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.38 Å2
2---1.28 Å20 Å2
3---0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12749 0 88 404 13241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913026
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213059
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.99317576
X-RAY DIFFRACTIONr_angle_other_deg0.759330175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6951673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34825.051487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.742152430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8081560
X-RAY DIFFRACTIONr_chiral_restr0.0720.22073
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022587
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_it1.873.4936710
X-RAY DIFFRACTIONr_mcbond_other1.8693.4936709
X-RAY DIFFRACTIONr_mcangle_it2.7595.238377
X-RAY DIFFRACTIONr_mcangle_other2.7595.238378
X-RAY DIFFRACTIONr_scbond_it2.3593.8366316
X-RAY DIFFRACTIONr_scbond_other2.3593.8366317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6795.6159200
X-RAY DIFFRACTIONr_long_range_B_refined4.82527.58614774
X-RAY DIFFRACTIONr_long_range_B_other4.82627.56814667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 378 -
Rwork0.248 7544 -
obs--96.11 %

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