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- PDB-9cq2: CtfAB E46D active site mutant hydrolase -

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Basic information

Entry
Database: PDB / ID: 9cq2
TitleCtfAB E46D active site mutant hydrolase
Components(3-oxoacid CoA-transferase, ...) x 2
KeywordsTRANSFERASE / Acetoacetate-CoA Transferase / active site mutant / thermophile
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: 2.2 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 19, 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)92,98913
Polymers92,6324
Non-polymers3569
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-114 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.368, 131.368, 158.423
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
11A-533-

HOH

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Components

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

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


Mass: 22987.959 Da / Num. of mol.: 2 / Mutation: E46D
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
#2: 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

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Non-polymers , 4 types, 609 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 3.73 Å3/Da / Density % sol: 67.05 %
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-BM / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47.19 Å / Num. obs: 70761 / % possible obs: 99.96 % / Redundancy: 14.4 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.186 / Rrim(I) all: 0.1929 / Net I/σ(I): 13.79
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.224 / Num. unique obs: 6936 / CC1/2: 0.785 / % possible all: 99.98

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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: 2.2→47.19 Å / SU ML: 0.2579 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 1993 2.83 %
Rwork0.1693 68490 -
obs0.1707 70483 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 18 600 7008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01216515
X-RAY DIFFRACTIONf_angle_d1.26538835
X-RAY DIFFRACTIONf_chiral_restr0.06661095
X-RAY DIFFRACTIONf_plane_restr0.01641120
X-RAY DIFFRACTIONf_dihedral_angle_d8.2336891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.29031350.24214653X-RAY DIFFRACTION96.13
2.25-2.310.27511390.22524812X-RAY DIFFRACTION98.88
2.31-2.380.2711400.21744819X-RAY DIFFRACTION99.26
2.38-2.460.31241410.21284809X-RAY DIFFRACTION99.02
2.46-2.550.2591420.20894836X-RAY DIFFRACTION99.06
2.55-2.650.23761410.1984848X-RAY DIFFRACTION99.38
2.65-2.770.28471410.19064853X-RAY DIFFRACTION99.38
2.77-2.910.30321420.18354866X-RAY DIFFRACTION99.54
2.91-3.10.22861430.18924904X-RAY DIFFRACTION99.61
3.1-3.340.27171430.1854907X-RAY DIFFRACTION99.86
3.34-3.670.20531440.15884946X-RAY DIFFRACTION99.84
3.67-4.20.17881440.13634965X-RAY DIFFRACTION99.84
4.2-5.290.1351470.11335033X-RAY DIFFRACTION99.9
5.29-47.190.18931510.1615239X-RAY DIFFRACTION99.58

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