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- PDB-8k1c: Structural insight into the role of acetyl-CoA acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 8k1c
TitleStructural insight into the role of acetyl-CoA acetyltransferase from Fusobacterium nucleatum
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / acetyl-CoA acetyltransferase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.894 Å
AuthorsHe, S.R. / Bai, X. / Zhang, J. / Zhao, Z.D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structural insight into the role of acetyl-CoA acetyltransferase from Fusobacterium nucleatum
Authors: He, S.R. / Bai, X.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)169,7644
Polymers169,7644
Non-polymers00
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-75 kcal/mol
Surface area50140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.049, 78.161, 105.327
Angle α, β, γ (deg.)103.88, 93.73, 110.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Acetyl-CoA acetyltransferase


Mass: 42440.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Gene: FN0495 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8RG24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 12% (v/v) PEG 3350, 0.1M Sodium carbonate pH 6.4, 0.16M magnesium chloride

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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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.894→35.7331 Å / Num. obs: 309369 / % possible obs: 85.76 % / Redundancy: 2.8 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 0.2
Reflection shellResolution: 1.894→1.962 Å / Num. unique obs: 110832 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.894→35.733 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 3266 1.9 %
Rwork0.1999 --
obs0.2007 172148 69.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.894→35.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11801 0 0 357 12158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811878
X-RAY DIFFRACTIONf_angle_d0.95716005
X-RAY DIFFRACTIONf_dihedral_angle_d2.7799933
X-RAY DIFFRACTIONf_chiral_restr0.0551873
X-RAY DIFFRACTIONf_plane_restr0.0062061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8942-1.92250.3631490.26482956X-RAY DIFFRACTION28
1.9225-1.95260.2808740.26083619X-RAY DIFFRACTION34
1.9526-1.98460.3197730.25894013X-RAY DIFFRACTION39
1.9846-2.01880.2635830.24314551X-RAY DIFFRACTION43
2.0188-2.05550.3165890.24155074X-RAY DIFFRACTION48
2.0555-2.0950.30211100.23865340X-RAY DIFFRACTION51
2.095-2.13780.31941130.23695980X-RAY DIFFRACTION57
2.1378-2.18430.27541190.22566276X-RAY DIFFRACTION60
2.1843-2.23510.22711170.22026663X-RAY DIFFRACTION63
2.2351-2.29090.24111550.21356838X-RAY DIFFRACTION66
2.2909-2.35290.29751370.21087095X-RAY DIFFRACTION67
2.3529-2.42210.27451370.21357512X-RAY DIFFRACTION72
2.4221-2.50030.25581580.22977914X-RAY DIFFRACTION75
2.5003-2.58960.25961730.22278482X-RAY DIFFRACTION81
2.5896-2.69320.23541740.21368935X-RAY DIFFRACTION84
2.6932-2.81580.27891800.21299092X-RAY DIFFRACTION87
2.8158-2.96420.25171790.22269305X-RAY DIFFRACTION89
2.9642-3.14980.27861920.22329529X-RAY DIFFRACTION91
3.1498-3.39280.26971780.20719864X-RAY DIFFRACTION93
3.3928-3.73390.23791830.18779896X-RAY DIFFRACTION95
3.7339-4.27340.19692060.15399768X-RAY DIFFRACTION93
4.2734-5.38110.1741880.1499991X-RAY DIFFRACTION95
5.3811-35.7330.21461990.185710189X-RAY DIFFRACTION97

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