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- PDB-3mdd: CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PI... -

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Basic information

Entry
Database: PDB / ID: 3mdd
TitleCRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE
ComponentsMEDIUM CHAIN ACYL-COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE
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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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
FLAVIN-ADENINE DINUCLEOTIDE / Medium-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsKim, J.-J.P. / Wang, M. / Paschke, R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate.
Authors: Kim, J.J. / Wang, M. / Paschke, R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structure of the Medium-Chain Acyl-Coa Dehydrogenase from Pig Liver Mitochondria at 3-Angstroms Resolution
Authors: Kim, J.-J.P. / Wu, J.
History
DepositionJul 13, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 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
Remark 700SHEET STRAND 4 OF SHEET 2 DOES NOT INCLUDE RESIDUE 229.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
B: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4104
Polymers84,8392
Non-polymers1,5712
Water2,990166
1
A: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
B: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
hetero molecules

A: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
B: MEDIUM CHAIN ACYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,8198
Polymers169,6774
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area22970 Å2
ΔGint-158 kcal/mol
Surface area50190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.820, 136.130, 106.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MEDIUM CHAIN ACYL-COA DEHYDROGENASE


Mass: 42419.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P41367, EC: 1.3.99.3
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 30930 / % possible obs: 84 % / Num. measured all: 138867 / Rmerge(I) obs: 0.047

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Processing

SoftwareName: GPRLSA / Classification: refinement
RefinementResolution: 2.4→6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.173 30930
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 106 166 6236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.18 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.021

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