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- PDB-1udy: Medium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 1udy
TitleMedium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA
ComponentsAcyl-CoA dehydrogenase, medium-chain specific
KeywordsOXIDOREDUCTASE / MCAD complex
Function / homology
Function and homology information


mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / medium-chain fatty acid catabolic process / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / carnitine biosynthetic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity ...mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / medium-chain fatty acid catabolic process / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / carnitine biosynthetic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / cardiac muscle cell differentiation / glycogen biosynthetic process / regulation of gluconeogenesis / fatty acid beta-oxidation / response to starvation / response to cold / post-embryonic development / liver development / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial matrix / axon / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
Medium-chain specific acyl-CoA dehydrogenase / : / 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 ...Medium-chain specific acyl-CoA dehydrogenase / : / 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, N-terminal domain / Acyl-CoA dehydrogenase, C-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 oxidase/dehydrogenase, middle domain superfamily / 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
3-THIAOCTANOYL-COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / Medium-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSatoh, A. / Nakajima, Y. / Miyahara, I. / Hirotsu, K. / Tanaka, T. / Nishina, Y. / Shiga, K. / Tamaoki, H. / Setoyama, C. / Miura, R.
CitationJournal: J.BIOCHEM.(TOKYO) / Year: 2003
Title: Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA ...Title: Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
Authors: Satoh, A. / Nakajima, Y. / Miyahara, I. / Hirotsu, K. / Tanaka, T. / Nishina, Y. / Shiga, K. / Tamaoki, H. / Setoyama, C. / Miura, R.
History
DepositionMay 7, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: Acyl-CoA dehydrogenase, medium-chain specific
B: Acyl-CoA dehydrogenase, medium-chain specific
C: Acyl-CoA dehydrogenase, medium-chain specific
D: Acyl-CoA dehydrogenase, medium-chain specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,91512
Polymers174,1264
Non-polymers6,7898
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22420 Å2
ΔGint-162 kcal/mol
Surface area52460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.0, 110.6, 147.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acyl-CoA dehydrogenase, medium-chain specific / MEDIUM-CHAIN ACYL-COA DEHYDROGENASE


Mass: 43531.520 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: liver / References: UniProt: P41367, EC: 1.3.99.3
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CS8 / 3-THIAOCTANOYL-COENZYME A


Type: RNA linking / Mass: 911.769 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H48N7O17P3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.29 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, Tris-acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17-8 mg/mlprotein1drop
210 mMTris-acetate1droppH7.0
310-14 %(w/v)PEG40001reservoir
410 mMTris-acetate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2002
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 53947 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 69.5
Reflection
*PLUS
Num. measured all: 201618 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 69.5 % / Num. unique obs: 4381 / Rmerge(I) obs: 0.209

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 2666 RANDOM
Rwork0.198 --
all-53909 -
obs-53160 -
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11903 0 440 251 12594
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d21.21
X-RAY DIFFRACTIONc_improper_angle_d0.873
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.347
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.252
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.876
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rfactor Rfree: 0.339 / Rfactor Rwork: 0.278

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