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- PDB-1buc: THREE-DIMENSIONAL STRUCTURE OF BUTYRYL-COA DEHYDROGENASE FROM MEG... -

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Basic information

Entry
Database: PDB / ID: 1buc
TitleTHREE-DIMENSIONAL STRUCTURE OF BUTYRYL-COA DEHYDROGENASE FROM MEGASPHAERA ELSDENII
ComponentsBUTYRYL-COA DEHYDROGENASEShort-chain acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / ACYL-COA DEHYDROGENASE SHORT-CHAIN ACYL-COA DEHYDROGENASE / FLAVOPROTEIN
Function / homology
Function and homology information


short-chain acyl-CoA dehydrogenase / butyryl-CoA dehydrogenase activity / acyl-CoA dehydrogenase activity / fatty acid metabolic process / flavin adenine dinucleotide 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 / Acyl-CoA dehydrogenase, short-chain specific
Similarity search - Component
Biological speciesMegasphaera elsdenii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsDjordjevic, S. / Pace, C.P. / Stankovich, M.T. / Kim, J.J.P.
CitationJournal: Biochemistry / Year: 1995
Title: Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii.
Authors: Djordjevic, S. / Pace, C.P. / Stankovich, M.T. / Kim, J.J.
History
DepositionSep 6, 1994Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: BUTYRYL-COA DEHYDROGENASE
B: BUTYRYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1806
Polymers82,9062
Non-polymers3,2744
Water0
1
A: BUTYRYL-COA DEHYDROGENASE
B: BUTYRYL-COA DEHYDROGENASE
hetero molecules

A: BUTYRYL-COA DEHYDROGENASE
B: BUTYRYL-COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,36112
Polymers165,8124
Non-polymers6,5498
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area27100 Å2
ΔGint-139 kcal/mol
Surface area46990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.800, 107.800, 153.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.994, 0.1084, 0.0143), (0.1084, 0.9941, -0.0037), (-0.0146, -0.0021, -0.9999)
Vector: 105.7486, -5.3269, 230.40823)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 B 1 - B 383 A 1 - A 383 0.355

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Components

#1: Protein BUTYRYL-COA DEHYDROGENASE / Short-chain acyl-CoA dehydrogenase


Mass: 41453.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megasphaera elsdenii (bacteria) / References: UniProt: Q06319, 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2120 mMpotassium phosphate1drop
360 mMBis-Tris acetate1drop
4190 mMammonium sulfate1drop
54.3 %PEG45001drop
650 %PEG45001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 25601 / % possible obs: 80 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 81262 / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.193 --
obs0.193 26003 80 %
Displacement parametersBiso mean: 19 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 214 0 6032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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