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- PDB-1f14: L-3-HYDROXYACYL-COA DEHYDROGENASE (APO) -

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Basic information

Entry
Database: PDB / ID: 1f14
TitleL-3-HYDROXYACYL-COA DEHYDROGENASE (APO)
ComponentsL-3-HYDROXYACYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE / L-3-hydroxyacyl-CoA (apoenzyme)
Function / homology
Function and homology information


Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of butanoyl-CoA to acetyl-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 / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / regulation of insulin secretion / NAD+ binding ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of butanoyl-CoA to acetyl-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 / 3-hydroxyacyl-CoA dehydrogenase activity / fatty acid beta-oxidation / regulation of insulin secretion / NAD+ binding / negative regulation of insulin secretion / Mitochondrial protein degradation / response to activity / response to insulin / positive regulation of cold-induced thermogenesis / transferase activity / 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 / 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
Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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


Theoretical massNumber of molelcules
Total (without water)67,7922
Polymers67,7922
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-28 kcal/mol
Surface area25910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.440, 86.970, 168.290
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 54.8 %
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: 2.3→20 Å / Num. all: 33237 / Num. obs: 33237 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.146 / Num. unique all: 3305 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementResolution: 2.3→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1346566.55 / 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
Rfree0.267 1610 5 %RANDOM
Rwork0.213 ---
all-32510 --
obs-32510 96.5 %-
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4462 0 0 287 4749
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.581.5
X-RAY DIFFRACTIONc_mcangle_it42
X-RAY DIFFRACTIONc_scbond_it4.262
X-RAY DIFFRACTIONc_scangle_it6.142.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 280 5.3 %
Rwork0.288 4999 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.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_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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