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- PDB-1rx0: Crystal structure of isobutyryl-CoA dehydrogenase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1rx0
TitleCrystal structure of isobutyryl-CoA dehydrogenase complexed with substrate/ligand.
ComponentsAcyl-CoA dehydrogenase family member 8, mitochondrial
KeywordsOXIDOREDUCTASE / flavoprotein / dehydrogenase / coenzyme A
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / valine catabolic process / acyl-CoA dehydrogenase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / lipid metabolic process / flavin adenine dinucleotide binding / mitochondrial matrix
Similarity search - Function
Isobutyryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / 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 ...Isobutyryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / 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
METHACRYLYL-COENZYME A / ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Isobutyryl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBattaile, K.P. / Nguyen, T.V. / Vockley, J. / Kim, J.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structures of Isobutyryl-CoA Dehydrogenase and Enzyme-Product Complex: COMPARISON WITH ISOVALERYL- AND SHORT-CHAIN ACYL-COA DEHYDROGENASES.
Authors: Battaile, K.P. / Nguyen, T.V. / Vockley, J. / Kim, J.J.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase family member 8, mitochondrial
B: Acyl-CoA dehydrogenase family member 8, mitochondrial
C: Acyl-CoA dehydrogenase family member 8, mitochondrial
D: Acyl-CoA dehydrogenase family member 8, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,90428
Polymers170,9874
Non-polymers5,91724
Water26,5181472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27900 Å2
ΔGint-97 kcal/mol
Surface area45830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.204, 134.343, 189.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the homotetramer in the asymmetric unit.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acyl-CoA dehydrogenase family member 8, mitochondrial / ACAD-8 / Isobutyryl-CoA dehydrogenase / Activator- recruited cofactor 42 kDa component / ARC42


Mass: 42746.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAD8, ARC42 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9UKU7, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors

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Non-polymers , 5 types, 1496 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-2MC / METHACRYLYL-COENZYME A / Methacrylyl-CoA


Mass: 835.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O17P3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1472 / 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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 5000 MME, tris-acetate, ammonium acetate, ethylene glycol, n-octyl-B-D-glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 19K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 271603 / Num. obs: 221777 / % possible obs: 94.8 % / Biso Wilson estimate: 17.4 Å2
Reflection shellResolution: 1.76→1.83 Å / % possible all: 61.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→50 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 941266.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 22161 10 %SHELLS
Rwork0.179 ---
all0.181 221777 --
obs0.179 221777 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.3446 Å2 / ksol: 0.380759 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---4.57 Å20 Å2
3---4.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11922 0 362 1500 13784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.76→1.87 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 2869 12.2 %
Rwork0.24 20732 -
obs--58.3 %

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