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- PDB-3owa: Crystal Structure of Acyl-CoA Dehydrogenase complexed with FAD fr... -

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Basic information

Entry
Database: PDB / ID: 3owa
TitleCrystal Structure of Acyl-CoA Dehydrogenase complexed with FAD from Bacillus anthracis
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-structure / beta-barrel / dehydrogenase / cytosol
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding / oxidoreductase activity
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
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Acyl-CoA dehydrogenase / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Acyl-CoA Dehydrogenase complexed with FAD from Bacillus anthracis
Authors: Kim, Y. / Maltseva, N. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
C: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,59226
Polymers267,1434
Non-polymers5,44922
Water38,6782147
1
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,48415
Polymers133,5712
Non-polymers2,91213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-67 kcal/mol
Surface area41760 Å2
MethodPISA
2
C: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,10811
Polymers133,5712
Non-polymers2,5369
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-47 kcal/mol
Surface area41920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.613, 98.028, 107.743
Angle α, β, γ (deg.)92.80, 106.63, 105.30
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acyl-CoA dehydrogenase /


Mass: 66785.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS4875, BA_5246, GBAA5246, GBAA_5246 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q81XJ1, UniProt: A0A6H3ADM7*PLUS, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors

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Non-polymers , 6 types, 2169 molecules

#2: 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
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2147 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Ammonium sulfate 0.05 M BIS-TRIS pH6.5, 30 % v/v Pentaerythritol ethoxylate (15/4 EO/OH), VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 195135 / Num. obs: 195135 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.054 / Net I/σ(I): 12.1
Reflection shellResolution: 1.97→2 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.03 / Rsym value: 0.44 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-3000data collection
BALBESphasing
PHENIXrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 2Z1Q

2z1q


Resolution: 1.97→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.007 / SU ML: 0.102 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20131 9842 5 %RANDOM
Rwork0.1622 ---
obs0.16417 185170 96.92 %-
all-185170 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å21.16 Å22.1 Å2
2--0.06 Å23.62 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18051 0 362 2147 20560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02219100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.99625771
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16752398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66824.903824
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.647153513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.20315100
X-RAY DIFFRACTIONr_chiral_restr0.1040.22884
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9791.511736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.833218860
X-RAY DIFFRACTIONr_scbond_it3.99337364
X-RAY DIFFRACTIONr_scangle_it5.6494.56911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.967→2.018 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 672 -
Rwork0.266 12637 -
obs--89.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61040.1718-0.2750.8516-0.41430.4937-0.0807-0.0203-0.1416-0.1932-0.076-0.28360.15230.02790.15670.12430.01010.05690.059-0.00050.12422.58510.7773-1.7846
20.8942-0.05760.00710.7446-0.30720.43480.0410.01470.30070.0125-0.0152-0.1095-0.0485-0.0387-0.02590.0714-0.01160.00730.0408-0.0020.1456-7.8635.4607-4.8298
30.77060.23950.06060.5685-0.26350.4158-0.05030.11870.0066-0.10020.1410.07390.0159-0.1529-0.09080.101-0.0067-0.00940.1458-0.0040.0461-43.237-27.380829.6092
41.16030.30940.29790.9172-0.10720.6260.1309-0.3197-0.27380.188-0.0444-0.20150.0073-0.1404-0.08650.1073-0.0146-0.04880.14970.05240.0987-28.1068-40.828960.1236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 600
2X-RAY DIFFRACTION2B1 - 600
3X-RAY DIFFRACTION3C1 - 600
4X-RAY DIFFRACTION4D1 - 600

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