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- PDB-4eu8: Succinyl-CoA:acetate CoA-transferase (AarCH6-S71A) in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 4eu8
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6-S71A) in complex with CoA
ComponentsSuccinyl-CoA:acetate coenzyme A transferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


succinyl-CoA:acetate CoA-transferase / acetate catabolic process / acetyl-CoA hydrolase activity / acetate CoA-transferase activity / succinyl-CoA catabolic process / acetyl-CoA biosynthetic process from acetate / transferase activity
Similarity search - Function
Succinate CoA transferase / 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
COENZYME A / Succinyl-CoA:acetate CoA-transferase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.809 Å
AuthorsMullins, E.A. / Kappock, T.J.
Citation
Journal: Biochemistry / Year: 2012
Title: Crystal Structures of Acetobacter aceti Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase Reveal Specificity Determinants and Illustrate the Mechanism Used by Class I CoA-Transferases.
Authors: Mullins, E.A. / Kappock, T.J.
#1: Journal: J.Bacteriol. / Year: 2008
Title: A specialized citric acid cycle requiring succinyl-coenzyme A (CoA):acetate CoA-transferase (AarC) confers acetic acid resistance on the acidophile Acetobacter aceti
Authors: Mullins, E.A. / Francois, J.A. / Kappock, T.J.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinyl-CoA:acetate coenzyme A transferase
B: Succinyl-CoA:acetate coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7378
Polymers112,0612
Non-polymers1,6776
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-77 kcal/mol
Surface area32850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.276, 109.667, 120.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Succinyl-CoA:acetate coenzyme A transferase


Mass: 56030.289 Da / Num. of mol.: 2 / Mutation: S71A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Gene: aarC / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: B3EY95, succinyl-CoA:acetate CoA-transferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.9 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, and 2 mM CoA, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.809→50 Å / Num. all: 81762 / Num. obs: 81672 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Χ2: 1.371 / Net I/σ(I): 40.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.81-1.8411.70.4825.940050.4820.786100
1.84-1.8711.60.409740370.4090.798100
1.87-1.9111.70.3438.440320.3430.84100
1.91-1.9511.80.3099.640300.3090.907100
1.95-1.9911.80.25211.540530.2520.869100
1.99-2.0411.80.21113.740240.2110.89899.9
2.04-2.0911.80.19415.640380.1940.98499.9
2.09-2.1511.80.15818.940780.1580.974100
2.15-2.2111.90.13921.740100.1391.012100
2.21-2.2811.90.13323.540530.1331.129100
2.28-2.3611.90.11626.340590.1161.098100
2.36-2.46120.10130.740640.1011.142100
2.46-2.5712.10.0933440920.0931.225100
2.57-2.712.20.08438.440990.0841.284100
2.7-2.8712.20.0774440780.0771.464100
2.87-3.0912.20.07551.140840.0751.91100
3.09-3.4111.80.06962.441290.0692.669100
3.41-3.911.50.0617341440.0613.078100
3.9-4.9111.90.04582.941910.0452.486100
4.91-5011.30.0357743720.0351.74899.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.809→34.69 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.2 / σ(F): 0 / Phase error: 21.96 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 4077 5 %RANDOM
Rwork0.1804 ---
obs0.1826 81593 99.76 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.413 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 76.36 Å2 / Biso mean: 20.8142 Å2 / Biso min: 5.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.2692 Å20 Å2-0 Å2
2--1.5243 Å20 Å2
3----3.7934 Å2
Refinement stepCycle: LAST / Resolution: 1.809→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7682 0 100 689 8471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077976
X-RAY DIFFRACTIONf_angle_d1.11110822
X-RAY DIFFRACTIONf_chiral_restr0.0731193
X-RAY DIFFRACTIONf_plane_restr0.0051433
X-RAY DIFFRACTIONf_dihedral_angle_d15.083070
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8085-1.82980.29551280.240424642592259294
1.8298-1.85210.28021390.2322264727862786100
1.8521-1.87550.29171400.221265627962796100
1.8755-1.90020.29881370.216262727642764100
1.9002-1.92630.28311400.206264527852785100
1.9263-1.95380.25011400.2011265827982798100
1.9538-1.98290.2661400.1936265327932793100
1.9829-2.01390.27461390.1952264127802780100
2.0139-2.04690.24711390.2011266228012801100
2.0469-2.08220.27441390.1975263227712771100
2.0822-2.12010.25371400.1913266228022802100
2.1201-2.16080.2271390.1809264727862786100
2.1608-2.20490.26061390.19265427932793100
2.2049-2.25290.25031420.195269328352835100
2.2529-2.30530.26461400.1858264227822782100
2.3053-2.36290.23941390.1923265527942794100
2.3629-2.42680.22531420.1775268728292829100
2.4268-2.49820.21121410.177268828292829100
2.4982-2.57880.21661400.1724265927992799100
2.5788-2.67090.22381410.1825269328342834100
2.6709-2.77780.22771400.1872265927992799100
2.7778-2.90420.2241420.1806268428262826100
2.9042-3.05720.25651430.1899272128642864100
3.0572-3.24860.21561410.186267228132813100
3.2486-3.49920.18991410.1695269828392839100
3.4992-3.8510.20811430.1606271828612861100
3.851-4.40730.18871450.15274728922892100
4.4073-5.5490.19381460.1547276429102910100
5.549-34.6960.17771520.1771288830403040100

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