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- PDB-4eu6: Succinyl-CoA:acetate CoA-transferase (AarCH6) in complex with CoA... -

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Basic information

Entry
Database: PDB / ID: 4eu6
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6) in complex with CoA, acetate, and covalent acetylglutamyl anhydride and glutamyl-CoA thioester adducts
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
ACETATE ION / COENZYME A / Succinyl-CoA:acetate CoA-transferase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 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 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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)113,88810
Polymers112,0932
Non-polymers1,7958
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-72 kcal/mol
Surface area32030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.168, 110.414, 119.823
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: 56046.289 Da / Num. of mol.: 2
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 37.94 %
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 acetyl-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: 1.988→50 Å / Num. all: 61848 / Num. obs: 61848 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Χ2: 1.404 / Net I/σ(I): 34.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.99-2.0212.10.537.230220.530.8899.1
2.02-2.0612.10.5027.930160.5020.9199.4
2.06-2.1120.4589.130580.4580.98199.3
2.1-2.1412.10.39210.630340.3920.9799.5
2.14-2.1912.10.35611.930230.3560.98999.1
2.19-2.2412.10.33611.930520.3361.01199.6
2.24-2.312.10.31313.430860.3131.13599.6
2.3-2.3612.10.28113.930400.2811.01699.4
2.36-2.4312.20.23916.130560.2391.02599.5
2.43-2.5112.20.21617.930660.2161.09499.8
2.51-2.612.30.19519.631080.1951.13599.7
2.6-2.712.50.18322.430660.1831.34799.9
2.7-2.8212.70.16425.130880.1641.495100
2.82-2.9712.90.13830.530800.1381.788100
2.97-3.1613.20.12335.731250.1232.024100
3.16-3.413.60.09746.631240.0972.301100
3.4-3.74140.07359.531230.0732.261100
3.74-4.2914.20.05370.631540.0531.954100
4.29-5.414.10.04378.931810.0431.73100
5.4-5013.40.03675.133460.0361.499.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.988→34.745 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.47 / σ(F): 0 / Phase error: 20.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 3092 5.01 %RANDOM
Rwork0.1644 ---
obs0.1666 61777 99.6 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.618 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso max: 80.03 Å2 / Biso mean: 22.8315 Å2 / Biso min: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.1168 Å20 Å2-0 Å2
2--4.5971 Å20 Å2
3----3.4803 Å2
Refinement stepCycle: LAST / Resolution: 1.988→34.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7767 0 107 595 8469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078047
X-RAY DIFFRACTIONf_angle_d1.04710914
X-RAY DIFFRACTIONf_chiral_restr0.0691200
X-RAY DIFFRACTIONf_plane_restr0.0051446
X-RAY DIFFRACTIONf_dihedral_angle_d15.4233077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.9878-2.01890.24311410.165425492690269097
2.0189-2.0520.23511280.171926262754275499
2.052-2.08730.22181380.175526172755275599
2.0873-2.12530.24771450.168826312776277699
2.1253-2.16620.23461300.171626482778277899
2.1662-2.21040.23121500.16925882738273899
2.2104-2.25840.2221410.171726692810281099
2.2584-2.31090.23641440.1713261227562756100
2.3109-2.36870.26381380.1701264527832783100
2.3687-2.43280.21041310.167726452776277699
2.4328-2.50430.19111380.1638265627942794100
2.5043-2.58510.23661520.1701265628082808100
2.5851-2.67750.22881280.1862266427922792100
2.6775-2.78470.24371440.1837266028042804100
2.7847-2.91130.21661410.1782268628272827100
2.9113-3.06470.21921330.1792269628292829100
3.0647-3.25660.20381540.1671266528192819100
3.2566-3.50780.19431290.1605269628252825100
3.5078-3.86040.2091490.1491269028392839100
3.8604-4.41810.15631410.1443275128922892100
4.4181-5.56260.18191470.1459274728942894100
5.5626-34.75020.18881500.1675288830383038100

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