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- PDB-1f12: L-3-HYDROXYACYL-COA DEHYDROGENASE COMPLEXED WITH 3-HYDROXYBUTYRYL-COA -

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Basic information

Entry
Database: PDB / ID: 1f12
TitleL-3-HYDROXYACYL-COA DEHYDROGENASE COMPLEXED WITH 3-HYDROXYBUTYRYL-COA
ComponentsL-3-HYDROXYACYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE / L-3-hydroxyacyl-CoA complexed with 3-hydroxybutyryl-CoA
Function / homology
Function and homology information


Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / fatty acid beta-oxidation / NAD+ binding / Mitochondrial protein degradation ...Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / fatty acid beta-oxidation / NAD+ binding / Mitochondrial protein degradation / regulation of insulin secretion / response to activity / negative regulation of insulin secretion / response to insulin / transferase activity / positive regulation of cold-induced thermogenesis / spermatogenesis / cell differentiation / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
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 ...: / 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-HYDROXYBUTANOYL-COENZYME A / Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBarycki, J.J. / O'Brien, L.K. / Strauss, A.W. / Banaszak, L.J.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Sequestration of the active site by interdomain shifting. Crystallographic and spectroscopic evidence for distinct conformations of L-3-hydroxyacyl-CoA dehydrogenase.
Authors: Barycki, J.J. / O'Brien, L.K. / Strauss, A.W. / Banaszak, L.J.
#1: Journal: Biochemistry / Year: 1999
Title: Biochemical Characterization and Crystal Structure Determination of Human Heart Short Chain L-3-hydroxyacyl-CoA Dehydrogenase Provide Insights into Catalytic Mechanism
Authors: Barycki, J.J. / O'Brien, L.K. / Bratt, J.M. / Zhang, R. / Sanishvili, R. / Strauss, A.W. / Banaszak, L.J.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-3-HYDROXYACYL-COA DEHYDROGENASE
B: L-3-HYDROXYACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6453
Polymers67,7922
Non-polymers8541
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-22 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.040, 88.100, 167.220
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 L-3-HYDROXYACYL-COA DEHYDROGENASE / SCHAD


Mass: 33895.824 Da / Num. of mol.: 2 / Mutation: F80C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: PROTEIN WAS EXPRESSED WITH A C-TERMINAL HEXAMERIC HISTIDINE TAG.
Organ: HEART / Plasmid: PET28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q16836, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-3HC / 3-HYDROXYBUTANOYL-COENZYME A / 3-HYDROXYBUTYRYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O18P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM N-[2-acetamido]-2-iminodiacetic acid within the precipitant range of 14% to 19% polyethylene glycol 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: Barycki, J.J., (1999) Biochemistry, 38, 5786.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
25 mMNAD+1drop
350 mMN-[2-acetamido]-2-iminodiacetic acid1reservoir
414-19 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03321
DetectorType: APS-1 / Detector: CCD / Date: Feb 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 29550 / Num. obs: 29550 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.474 / Num. unique all: 2908 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementResolution: 2.4→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 689257.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1374 4.9 %RANDOM
Rwork0.212 ---
all-28274 --
obs-28274 95.2 %-
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 54 187 4713
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it31.5
X-RAY DIFFRACTIONc_mcangle_it4.662
X-RAY DIFFRACTIONc_scbond_it4.712
X-RAY DIFFRACTIONc_scangle_it6.712.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 212 5 %
Rwork0.333 4050 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CAA_IDEAL_50.PARCAA.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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