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- PDB-9vag: Crystal structure of CoA transferase from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 9vag
TitleCrystal structure of CoA transferase from Thermus thermophilus
Components4-hydroxybutyrate coenzyme A transferase
KeywordsTRANSFERASE / CoA transferase
Function / homology
Function and homology information


acetate CoA-transferase activity / acetate metabolic process
Similarity search - Function
Acetyl-CoA hydrolase/transferase, N-terminal / Acetyl-CoA hydrolase/transferase C-terminal domain / Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily / Acetyl-CoA hydrolase/transferase / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / NagB/RpiA transferase-like
Similarity search - Domain/homology
4-hydroxybutyrate coenzyme A transferase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsYoshida, A. / Yamamoto, H. / Nishiyama, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17J40083 Japan
Japan Society for the Promotion of Science (JSPS)20K05804 Japan
CitationJournal: To Be Published
Title: Catalytic regulation of CoA transferase by an NAD+-sensing accessory protein and protein acetylation
Authors: Yoshida, A. / Yamamoto, H. / Nishiyama, M.
History
DepositionJun 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 4-hydroxybutyrate coenzyme A transferase
H: 4-hydroxybutyrate coenzyme A transferase
A: 4-hydroxybutyrate coenzyme A transferase
B: 4-hydroxybutyrate coenzyme A transferase
C: 4-hydroxybutyrate coenzyme A transferase
D: 4-hydroxybutyrate coenzyme A transferase
E: 4-hydroxybutyrate coenzyme A transferase
G: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)394,4128
Polymers394,4128
Non-polymers00
Water1,00956
1
F: 4-hydroxybutyrate coenzyme A transferase
H: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)98,6032
Polymers98,6032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-10 kcal/mol
Surface area29460 Å2
MethodPISA
2
A: 4-hydroxybutyrate coenzyme A transferase
B: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)98,6032
Polymers98,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-10 kcal/mol
Surface area29530 Å2
MethodPISA
3
C: 4-hydroxybutyrate coenzyme A transferase
D: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)98,6032
Polymers98,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-11 kcal/mol
Surface area29770 Å2
MethodPISA
4
E: 4-hydroxybutyrate coenzyme A transferase
G: 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)98,6032
Polymers98,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-8 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.342, 147.380, 171.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
4-hydroxybutyrate coenzyme A transferase


Mass: 49301.562 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1083 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72IP9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 3350, 6% MPD, 0.1M lithium sulfate, 0.05M imidazole, pH 6.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→48.78 Å / Num. obs: 109953 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.983 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.072 / Rrim(I) all: 0.179 / Χ2: 1.11 / Net I/σ(I): 6.6 / Num. measured all: 722996
Reflection shellResolution: 2.63→2.67 Å / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.962 / Num. measured all: 37579 / Num. unique obs: 5395 / CC1/2: 0.876 / Rpim(I) all: 0.39 / Rrim(I) all: 1.038 / Χ2: 0.86 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OAS

2oas


Resolution: 2.63→47.26 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.827 / SU B: 17.164 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.34713 5326 5 %RANDOM
Rwork0.28264 ---
obs0.28588 102091 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.977 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0 Å20 Å2
2---1.65 Å2-0 Å2
3---3.23 Å2
Refinement stepCycle: 1 / Resolution: 2.63→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25689 0 0 56 25745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01226309
X-RAY DIFFRACTIONr_bond_other_d0.0010.01625395
X-RAY DIFFRACTIONr_angle_refined_deg2.6831.81835761
X-RAY DIFFRACTIONr_angle_other_deg0.941.74458300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.48153387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.5235246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.44104218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1480.24063
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0231646
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026018
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.9884.77113551
X-RAY DIFFRACTIONr_mcbond_other7.9884.77113551
X-RAY DIFFRACTIONr_mcangle_it11.228.56816934
X-RAY DIFFRACTIONr_mcangle_other11.228.56916935
X-RAY DIFFRACTIONr_scbond_it8.9165.42312758
X-RAY DIFFRACTIONr_scbond_other8.9165.42312759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.8719.62718827
X-RAY DIFFRACTIONr_long_range_B_refined15.50545.9128343
X-RAY DIFFRACTIONr_long_range_B_other15.50545.9128344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 351 -
Rwork0.333 7676 -
obs--99.91 %

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