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- PDB-9ctd: CtfAB F42TS45C mutant co-crystallized with acetyl-CoA -

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Basic information

Entry
Database: PDB / ID: 9ctd
TitleCtfAB F42TS45C mutant co-crystallized with acetyl-CoA
Components(3-oxoacid CoA-transferase, ...) x 2
KeywordsTRANSFERASE / Acetoacetate-CoA Transferase / thermophile / acetyl-CoA / 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 / COENZYME A / DI(HYDROXYETHYL)ETHER / 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: 1.9 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 24, 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
D: 3-oxoacid CoA-transferase, A subunit
A: 3-oxoacid CoA-transferase, A subunit
C: 3-oxoacid CoA-transferase, B subunit
B: 3-oxoacid CoA-transferase, B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,53921
Polymers92,6004
Non-polymers2,93917
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-35 kcal/mol
Surface area31970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.694, 130.694, 155.382
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
Components on special symmetry positions
IDModelComponents
11D-546-

HOH

21A-539-

HOH

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Components

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3-oxoacid CoA-transferase, ... , 2 types, 4 molecules DACB

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


Mass: 23328.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho melanesiensis (bacteria) / Gene: Tmel_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: A6LM40, acetate CoA-transferase
#2: Protein 3-oxoacid CoA-transferase, B subunit


Mass: 22971.980 Da / Num. of mol.: 2 / Mutation: F42T, S45C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho melanesiensis (bacteria) / Gene: Tmel_1135 / Production host: Escherichia coli (E. coli)
References: UniProt: A6LM39, butyrate-acetoacetate CoA-transferase

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Non-polymers , 4 types, 669 molecules

#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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.58 Å3/Da / Density % sol: 65.67 %
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: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→41.95 Å / Num. obs: 104715 / % possible obs: 98.72 % / Redundancy: 13.4 % / Biso Wilson estimate: 17.53 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.146 / Rrim(I) all: 0.152 / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10118 / CC1/2: 0.913 / Rrim(I) all: 0.644 / % possible all: 96.94

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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: 1.9→41.95 Å / SU ML: 0.152 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.1846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1767 1982 1.89 %
Rwork0.1507 102733 -
obs0.1512 104715 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6400 0 164 652 7216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01176680
X-RAY DIFFRACTIONf_angle_d1.27439042
X-RAY DIFFRACTIONf_chiral_restr0.07141099
X-RAY DIFFRACTIONf_plane_restr0.01111127
X-RAY DIFFRACTIONf_dihedral_angle_d9.9491020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.24421370.18897075X-RAY DIFFRACTION96.29
1.95-20.22221370.16827117X-RAY DIFFRACTION97.58
2-2.060.19141390.16197227X-RAY DIFFRACTION98.2
2.06-2.120.20151400.15667218X-RAY DIFFRACTION98.32
2.12-2.20.18871400.15537246X-RAY DIFFRACTION98.47
2.2-2.290.16251400.14687274X-RAY DIFFRACTION98.81
2.29-2.390.18661410.13987320X-RAY DIFFRACTION99.03
2.39-2.520.15821420.13917311X-RAY DIFFRACTION99.06
2.52-2.680.16941430.13767357X-RAY DIFFRACTION99.34
2.68-2.880.16551410.14937385X-RAY DIFFRACTION99.41
2.88-3.170.19941430.1637418X-RAY DIFFRACTION99.5
3.17-3.630.20011430.16317454X-RAY DIFFRACTION99.48
3.63-4.580.12971460.12877524X-RAY DIFFRACTION99.53
4.58-41.950.17721500.15357807X-RAY DIFFRACTION99

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