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- PDB-8k9h: Complex structure of Acetoacetate:butyrate/acetate coenzyme A tra... -

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Basic information

Entry
Database: PDB / ID: 8k9h
TitleComplex structure of Acetoacetate:butyrate/acetate coenzyme A transferase and Butyrate-acetoacetate CoA-transferase subunit B from Fusobacterium nucleatum ATCC 25586
Components
  • Acetoacetate:butyrate/acetate coenzyme A transferase
  • Butyrate-acetoacetate CoA-transferase subunit B
KeywordsTRANSFERASE / coenzyme A transferase / CoA-transferase subunit B / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


butyrate-acetoacetate CoA-transferase / butyrate-acetoacetate CoA-transferase activity / CoA-transferase activity
Similarity search - Function
3-oxoacid CoA-transferase, subunit A / 3-oxoacid CoA-transferase, subunit B / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Acetoacetate:butyrate/acetate coenzyme A transferase / Butyrate-acetoacetate CoA-transferase subunit B
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsBai, X. / Zhao, Z.D. / Xu, Y.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: To Be Published
Title: Complex structure of Acetoacetate:butyrate/acetate coenzyme A transferase and Butyrate-acetoacetate CoA-transferase subunit B from Fusobacterium nucleatum ATCC 25586
Authors: Bai, X. / Zhao, Z.D. / Xu, Y.B.
History
DepositionAug 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Butyrate-acetoacetate CoA-transferase subunit B
B: Acetoacetate:butyrate/acetate coenzyme A transferase
C: Butyrate-acetoacetate CoA-transferase subunit B
D: Acetoacetate:butyrate/acetate coenzyme A transferase
E: Butyrate-acetoacetate CoA-transferase subunit B
F: Acetoacetate:butyrate/acetate coenzyme A transferase
G: Butyrate-acetoacetate CoA-transferase subunit B
H: Acetoacetate:butyrate/acetate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,90110
Polymers189,7088
Non-polymers1922
Water4,504250
1
A: Butyrate-acetoacetate CoA-transferase subunit B
B: Acetoacetate:butyrate/acetate coenzyme A transferase
G: Butyrate-acetoacetate CoA-transferase subunit B
H: Acetoacetate:butyrate/acetate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9505
Polymers94,8544
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-89 kcal/mol
Surface area29300 Å2
MethodPISA
2
C: Butyrate-acetoacetate CoA-transferase subunit B
D: Acetoacetate:butyrate/acetate coenzyme A transferase
E: Butyrate-acetoacetate CoA-transferase subunit B
F: Acetoacetate:butyrate/acetate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9505
Polymers94,8544
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-96 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.518, 166.518, 191.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Butyrate-acetoacetate CoA-transferase subunit B


Mass: 23226.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: FN1856 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RHY4, butyrate-acetoacetate CoA-transferase
#2: Protein
Acetoacetate:butyrate/acetate coenzyme A transferase


Mass: 24201.088 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: FN1857 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RHY3, butyrate-acetoacetate CoA-transferase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 4.22 Å3/Da / Density % sol: 70.86 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 10.5 / Details: Ammonium sulfate,Lithium sulfate,Caps pH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.73→48.07 Å / Num. obs: 79588 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.994 / Rrim(I) all: 0.247 / Net I/σ(I): 7.5
Reflection shellResolution: 2.73→2.78 Å / Rmerge(I) obs: 1.003 / Num. unique obs: 7920

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→48.07 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1982 2.49 %
Rwork0.1951 --
obs0.1959 79588 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12034 0 10 250 12294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912211
X-RAY DIFFRACTIONf_angle_d1.03416648
X-RAY DIFFRACTIONf_dihedral_angle_d4.3017558
X-RAY DIFFRACTIONf_chiral_restr0.0592090
X-RAY DIFFRACTIONf_plane_restr0.0062138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.7980.3281420.30285459X-RAY DIFFRACTION100
2.798-2.87370.36551430.28585560X-RAY DIFFRACTION100
2.8737-2.95820.31511430.27315547X-RAY DIFFRACTION100
2.9582-3.05370.3341430.25775515X-RAY DIFFRACTION100
3.0537-3.16280.28191420.24535524X-RAY DIFFRACTION100
3.1628-3.28940.30631430.23785537X-RAY DIFFRACTION100
3.2894-3.43910.2611370.2275533X-RAY DIFFRACTION100
3.4391-3.62030.2791470.2015579X-RAY DIFFRACTION100
3.6203-3.84710.21471410.18995528X-RAY DIFFRACTION100
3.8471-4.1440.22311440.17415534X-RAY DIFFRACTION100
4.144-4.56070.16961380.1525554X-RAY DIFFRACTION100
4.5607-5.21990.17911380.15255571X-RAY DIFFRACTION100
5.2199-6.57390.21771430.18895572X-RAY DIFFRACTION100
6.5739-48.070.17641380.17365593X-RAY DIFFRACTION99

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