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- PDB-8i4p: crystal structure of Acyl-CoA dehydrogenase from Thermobifida fusca -

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Basic information

Entry
Database: PDB / ID: 8i4p
Titlecrystal structure of Acyl-CoA dehydrogenase from Thermobifida fusca
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / 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
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesThermobifida fusca YX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChoi, M. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Acyl-CoA dehydrogenase from Thermobifida fusca
Authors: Choi, M. / Kim, K.
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)44,2894
Polymers43,3191
Non-polymers9703
Water3,063170
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)177,15416
Polymers173,2754
Non-polymers3,87912
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 area26160 Å2
ΔGint-168 kcal/mol
Surface area47670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.721, 101.721, 311.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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 YX (bacteria) / Gene: Tfu_1647 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47PD7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 4.66 Å3/Da / Density % sol: 73.59 %
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: 293 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 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 64134 / % possible obs: 98.8 % / Redundancy: 9.2 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.024 / Rrim(I) all: 0.08 / Χ2: 1.721 / Net I/σ(I): 11.1 / Num. measured all: 592579
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.935.90.34731430.8050.9450.1430.3771.12798.6
1.93-1.976.30.31531470.8750.9660.1270.3411.23998.8
1.97-2.016.70.29131720.9210.9790.1120.3131.30299.1
2.01-2.0570.2731650.9550.9890.1010.2891.37498.9
2.05-2.097.20.25731750.9560.9890.0950.2751.36899.1
2.09-2.147.70.22631640.9840.9960.080.2411.48999.3
2.14-2.197.90.20331890.9780.9940.070.2161.50599.1
2.19-2.258.40.18131780.9860.9960.0610.1921.698.8
2.25-2.328.50.16831580.9890.9970.0560.1781.61698.4
2.32-2.398.80.15231520.9930.9980.050.161.64798.7
2.39-2.4890.14431940.9920.9980.0470.1521.64898.7
2.48-2.589.60.12731730.9950.9990.040.1341.67498.5
2.58-2.79.90.11431690.9950.9990.0350.121.68998.5
2.7-2.8410.30.132270.9970.9990.030.1051.74298.8
2.84-3.0210.80.08632060.9980.9990.0260.091.79598.9
3.02-3.2511.40.07232240.99810.0210.0751.82998.8
3.25-3.5811.90.0632330.99810.0170.0631.90999
3.58-4.0912.40.05132710.99910.0140.0532.03499
4.09-5.1612.60.04833110.99910.0140.052.09999.2
5.16-5011.90.05134830.9960.9990.0150.0542.24998.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.403 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19624 3221 5 %RANDOM
Rwork0.17938 ---
obs0.18024 60908 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: 26.792 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å2-0 Å20 Å2
2--1.43 Å2-0 Å2
3----2.85 Å2
Refinement stepCycle: 1 / Resolution: 1.9→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 65 170 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133051
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152868
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.6464129
X-RAY DIFFRACTIONr_angle_other_deg1.5141.5826589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37121.19168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6615506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8791528
X-RAY DIFFRACTIONr_chiral_restr0.0940.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
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_it2.2892.5331523
X-RAY DIFFRACTIONr_mcbond_other2.2832.531522
X-RAY DIFFRACTIONr_mcangle_it2.9263.7851902
X-RAY DIFFRACTIONr_mcangle_other2.9263.7871903
X-RAY DIFFRACTIONr_scbond_it4.1583.0391528
X-RAY DIFFRACTIONr_scbond_other4.1613.041525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1464.3742228
X-RAY DIFFRACTIONr_long_range_B_refined6.72130.7833538
X-RAY DIFFRACTIONr_long_range_B_other6.6830.6913527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 206 -
Rwork0.319 4443 -
obs--97.81 %

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