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- PDB-9csc: CtfAB Native Acetoacetate-CoA Transferase protein -

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Open data


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Basic information

Entry
Database: PDB / ID: 9csc
TitleCtfAB Native Acetoacetate-CoA Transferase protein
Components
  • 3-oxoacid CoA-transferase, A subunit
  • 3-oxoacid CoA-transferase, B subunit
KeywordsTRANSFERASE / Acetoacetate-CoA Transferase / thermophile / acetate binding site
Function / homology
Function and homology information


butyrate-acetoacetate CoA-transferase / butyrate-acetoacetate CoA-transferase activity / acetate CoA-transferase / acetate CoA-transferase activity
Similarity search - Function
3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / 3-oxoacid CoA-transferase, subunit B / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like
Similarity search - Domain/homology
ACETATE ION / 3-oxoacid CoA-transferase, B subunit / 3-oxoacid CoA-transferase, A subunit
Similarity search - Component
Biological speciesThermosipho melanesiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBuhrman, G. / Bing, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0022192 United States
CitationJournal: Biochem.J. / Year: 2025
Title: Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile Thermosipho melanesiensis.
Authors: Bing, R.G. / Buhrman, G.K. / Ford, K.C. / Straub, C.T. / Laemthong, T. / Rose, R.B. / Adams, M.W.W. / Kelly, R.M.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3-oxoacid CoA-transferase, B subunit
A: 3-oxoacid CoA-transferase, A subunit
C: 3-oxoacid CoA-transferase, B subunit
D: 3-oxoacid CoA-transferase, A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8978
Polymers92,6604
Non-polymers2364
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-71 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.421, 131.421, 158.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein 3-oxoacid CoA-transferase, B subunit


Mass: 23001.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CtfB native protein beta chain / Source: (gene. exp.) Thermosipho melanesiensis (bacteria) / Gene: Tmel_1135 / Production host: Escherichia coli (E. coli)
References: UniProt: A6LM39, butyrate-acetoacetate CoA-transferase
#2: Protein 3-oxoacid CoA-transferase, A subunit


Mass: 23328.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CtfA alpha subunit / Source: (gene. exp.) Thermosipho melanesiensis (bacteria) / Gene: Tmel_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: A6LM40, acetate CoA-transferase
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na Acetate (pH 4.9-5.5), 6-10% PEG 3350 / PH range: 4.9-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.23 Å / Num. obs: 93455 / % possible obs: 99.85 % / Redundancy: 13.6 % / Biso Wilson estimate: 23.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1359 / Rrim(I) all: 0.1412 / Net I/σ(I): 16.23
Reflection shellResolution: 2→2.075 Å / Rmerge(I) obs: 0.6419 / Mean I/σ(I) obs: 3.73 / Num. unique obs: 9111 / CC1/2: 0.838 / Rrim(I) all: 0.6656

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.36 Å / SU ML: 0.3063 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2856 1963 2.17 %
Rwork0.2224 88533 -
obs0.2238 90496 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.77 Å2
Refinement stepCycle: LAST / Resolution: 2→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6375 0 16 442 6833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01496492
X-RAY DIFFRACTIONf_angle_d1.46238810
X-RAY DIFFRACTIONf_chiral_restr0.07591098
X-RAY DIFFRACTIONf_plane_restr0.0131114
X-RAY DIFFRACTIONf_dihedral_angle_d8.1723892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.37331390.29766270X-RAY DIFFRACTION97.14
2.05-2.110.36961430.30076353X-RAY DIFFRACTION98.1
2.11-2.170.33961420.29626333X-RAY DIFFRACTION97.49
2.17-2.240.36191420.27986287X-RAY DIFFRACTION97.22
2.24-2.320.33961420.27296343X-RAY DIFFRACTION97.37
2.32-2.410.35631390.26436288X-RAY DIFFRACTION97.03
2.41-2.520.32611370.25596254X-RAY DIFFRACTION95.3
2.52-2.650.30821370.24426058X-RAY DIFFRACTION92.91
2.65-2.820.29431430.23616487X-RAY DIFFRACTION99.47
2.82-3.040.30291440.23356473X-RAY DIFFRACTION98.54
3.04-3.340.26351370.21976398X-RAY DIFFRACTION96.87
3.34-3.830.25571360.1986240X-RAY DIFFRACTION94.22
3.83-4.820.23661330.16736038X-RAY DIFFRACTION90.15
4.82-38.360.22191490.17036711X-RAY DIFFRACTION96.16

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