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- PDB-1jqi: Crystal Structure of Rat Short Chain Acyl-CoA Dehydrogenase Compl... -

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Basic information

Entry
Database: PDB / ID: 1jqi
TitleCrystal Structure of Rat Short Chain Acyl-CoA Dehydrogenase Complexed With Acetoacetyl-CoA
Componentsshort chain acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / ENZYME-INHIBITOR COMPLEX
Function / homology
Function and homology information


Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / butyrate catabolic process / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / fatty acid beta-oxidation / response to starvation ...Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / butyrate catabolic process / short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / fatty acid beta-oxidation / response to starvation / response to glucocorticoid / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / Short-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBattaile, K.P. / Molin-Case, J. / Paschke, R. / Wang, M. / Bennett, D. / Vockley, J. / Kim, J.-J.P.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with acetoacetyl-CoA: comparison with other acyl-CoA dehydrogenases.
Authors: Battaile, K.P. / Molin-Case, J. / Paschke, R. / Wang, M. / Bennett, D. / Vockley, J. / Kim, J.J.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: short chain acyl-CoA dehydrogenase
B: short chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7136
Polymers84,4382
Non-polymers3,2744
Water4,684260
1
A: short chain acyl-CoA dehydrogenase
B: short chain acyl-CoA dehydrogenase
hetero molecules

A: short chain acyl-CoA dehydrogenase
B: short chain acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,42512
Polymers168,8774
Non-polymers6,5498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area28060 Å2
ΔGint-80 kcal/mol
Surface area48560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.610, 143.610, 77.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.5, -0.86603), (-0.86603, 0.5), (-1)0.00042, -0.00058, 77.45969

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Components

#1: Protein short chain acyl-CoA dehydrogenase


Mass: 42219.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pKK-223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P15651, EC: 1.3.99.2
#2: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 85 mM Tris-acetate, pH 7.0, 270 mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.8 mg/mlprotein1drop
285 mMTris-acetate1droppH7.0
3270 mMammonium sulfate1drop
485 mMTris-acetate1reservoirpH7.0
53.78 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 28, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 113237 / Biso Wilson estimate: 14.6 Å2
Reflection shellResolution: 2.1→30 Å / % possible all: 76.4
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. obs: 36527 / Num. measured all: 113237 / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
MERLOTphasing
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→29.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 495255.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2799 7.7 %RANDOM
Rwork0.168 ---
obs-36527 83.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.198 Å2 / ksol: 0.345391 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å22.56 Å20 Å2
2--0.54 Å20 Å2
3----1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5854 0 214 260 6328
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.431.5
X-RAY DIFFRACTIONc_mcangle_it3.482
X-RAY DIFFRACTIONc_scbond_it3.922
X-RAY DIFFRACTIONc_scangle_it5.422.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 380 7.7 %
Rwork0.198 4572 -
obs--68.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.7 % / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it2.431.5
X-RAY DIFFRACTIONc_scbond_it3.922
X-RAY DIFFRACTIONc_mcangle_it3.482
X-RAY DIFFRACTIONc_scangle_it5.422.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.255 / % reflection Rfree: 7.7 % / Rfactor Rwork: 0.198

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