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- PDB-4m9a: Crystal structure of Acyl-coA dehydrogenase from Burkholderia tha... -

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Basic information

Entry
Database: PDB / ID: 4m9a
TitleCrystal structure of Acyl-coA dehydrogenase from Burkholderia thailandensis E264
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / acyl-coA dehydrogenase / FAD / FADH2
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
Similarity search - Function
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 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Acyl-coA dehydrogenase from Burkholderia thailandensis E264
Authors: Lukacs, C.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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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)168,3385
Polymers167,5504
Non-polymers7881
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-83 kcal/mol
Surface area50210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 111.000, 170.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acyl-CoA dehydrogenase /


Mass: 41887.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_II1803 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2T4A2, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus a10: Buffer 3 pH 8.5, 0.06M divalents, 30% EDO_Peg8K, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 84670 / Num. obs: 83921 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.6 / Num. unique all: 6157 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UKW

1ukw


Resolution: 2.2→46.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.133 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23162 4186 5 %RANDOM
Rwork0.18627 ---
obs0.18855 79684 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2---1.07 Å2-0 Å2
3---2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11001 0 53 532 11586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911281
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210603
X-RAY DIFFRACTIONr_angle_refined_deg1.541.95915331
X-RAY DIFFRACTIONr_angle_other_deg0.849324223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0251482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16523.61482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.573151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6651588
X-RAY DIFFRACTIONr_chiral_restr0.0850.21739
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022597
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_it1.4022.2225943
X-RAY DIFFRACTIONr_mcbond_other1.3952.2215942
X-RAY DIFFRACTIONr_mcangle_it2.173.3227420
X-RAY DIFFRACTIONr_mcangle_other2.1723.3237421
X-RAY DIFFRACTIONr_scbond_it1.8682.4455338
X-RAY DIFFRACTIONr_scbond_other1.8672.4455338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9613.5937911
X-RAY DIFFRACTIONr_long_range_B_refined4.40417.95213222
X-RAY DIFFRACTIONr_long_range_B_other4.34617.83813082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 305 -
Rwork0.245 5836 -
obs--99.24 %
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)
10.28860.141-0.15340.68490.31820.39310.05-0.002-0.03250.0221-0.0745-0.0105-0.0082-0.06510.02450.0269-0.0217-0.01120.03490.00690.02842.3609-19.300162.0225
20.33310.08450.01680.34040.16550.0843-0.00680.0209-0.011-0.0243-0.02290.0399-0.0152-0.01440.02970.00950.0058-0.01290.0302-0.01250.0758-14.1949-18.327227.8442
30.33930.0149-0.0550.6821-0.10180.02580.02690.05520.0267-0.0712-0.0359-0.0010.0107-0.00090.00890.0319-0.00520.01310.03230.02220.05423.1808-2.25818.5767
40.1856-0.0919-0.0410.27460.11430.0764-0.0174-0.0127-0.0446-0.00080.024-0.0402-0.0094-0.0098-0.00660.00830.00170.00110.02530.00450.101733.1575-33.810639.0574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 377
2X-RAY DIFFRACTION2B2 - 377
3X-RAY DIFFRACTION3C2 - 377
4X-RAY DIFFRACTION4D2 - 377

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