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- PDB-8i4r: Crystal structure of Acyl-CoA dehydrogenase complexed with Acetyl... -

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Basic information

Entry
Database: PDB / ID: 8i4r
TitleCrystal structure of Acyl-CoA dehydrogenase complexed with Acetyl-CoA from Thermobifida fusca
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Acyl-CoA dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
ACETYL COENZYME *A / FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChoi, M. / Seok, J. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Acyl-CoA dehydrogenase complexed with Acetyl-CoA from Thermobifida fusca
Authors: Choi, M. / Kim, K.-J.
History
DepositionJan 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9143
Polymers43,3191
Non-polymers1,5952
Water1,29772
1
A: Acyl-CoA dehydrogenase
hetero molecules

A: Acyl-CoA dehydrogenase
hetero molecules

A: Acyl-CoA dehydrogenase
hetero molecules

A: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,65612
Polymers173,2754
Non-polymers6,3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area29290 Å2
ΔGint-159 kcal/mol
Surface area46010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.143, 102.143, 312.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

21A-572-

HOH

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Components

#1: Protein Acyl-CoA dehydrogenase /


Mass: 43318.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: strain YX / Gene: Tfu_1647 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47PD7
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.7 Å3/Da / Density % sol: 73.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate Sodium citrate Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 27192 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.089 / Χ2: 0.039 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.5-2.5470.31327091.9951100
2.54-2.597.10.29427132.0181100
2.59-2.647.20.27227182.091100
2.64-2.697.20.23826812.0491100
2.69-2.757.30.22127402.1151100
2.75-2.827.40.19726852.1571100
2.82-2.897.40.18527142.2151100
2.89-2.967.50.17127122.3231100
2.96-3.057.50.14327002.4121100
3.05-3.157.60.13526822.6221100
3.15-3.267.60.1227242.7611100
3.26-3.397.60.10627342.9411100
3.39-3.557.60.09726793.171100
3.55-3.737.60.08527523.3751100
3.73-3.977.60.07726813.6141100
3.97-4.277.50.07327123.7311100
4.27-4.77.50.06926993.761100
4.7-5.387.50.06627173.2111100
5.38-6.787.40.06927242.9811100
6.78-506.90.05926983.873199

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
REFMACv7.1.018refinement
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→32.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.951 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19488 1426 5 %RANDOM
Rwork0.16551 ---
obs0.16701 27192 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.744 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å2-0 Å2-0 Å2
2--2.3 Å2-0 Å2
3----4.6 Å2
Refinement stepCycle: 1 / Resolution: 2.51→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 104 72 3108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162790
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.6494198
X-RAY DIFFRACTIONr_angle_other_deg0.6051.5566488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.4319.51631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37610506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02612
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_it2.6112.9151524
X-RAY DIFFRACTIONr_mcbond_other2.5922.9141523
X-RAY DIFFRACTIONr_mcangle_it3.6244.3641902
X-RAY DIFFRACTIONr_mcangle_other3.6234.3671903
X-RAY DIFFRACTIONr_scbond_it4.5023.5221570
X-RAY DIFFRACTIONr_scbond_other4.5033.5241571
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4065.1062297
X-RAY DIFFRACTIONr_long_range_B_refined7.23537.873503
X-RAY DIFFRACTIONr_long_range_B_other7.23637.8713502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.571 Å
RfactorNum. reflection% reflection
Rfree0.207 101 -
Rwork0.201 1935 -
obs--97.37 %

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