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- PDB-4eud: Succinyl-CoA:acetate CoA-transferase (AarC) in complex with CoA a... -

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Basic information

Entry
Database: PDB / ID: 4eud
TitleSuccinyl-CoA:acetate CoA-transferase (AarC) in complex with CoA and citrate
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
CITRIC ACID / COENZYME A / Succinyl-CoA:acetate CoA-transferase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)111,6459
Polymers109,7762
Non-polymers1,8697
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-76 kcal/mol
Surface area33490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.653, 110.596, 119.923
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: 54888.070 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
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: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 2, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 64164 / Num. obs: 64164 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.214 / Rsym value: 0.214 / Χ2: 3.427 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.94-2.016.50.63.961360.61.37794.8
2.01-2.097.20.5425.762310.5421.77695.5
2.09-2.187.80.506662940.5062.31396.3
2.18-2.38.30.4597.562670.4592.36796.4
2.3-2.448.70.4199.563610.4192.42197.1
2.44-2.639.50.40512.663770.4053.2997.3
2.63-2.910.70.38717.164380.3873.84698
2.9-3.3211.80.28924.265870.2896.46699.5
3.32-4.1811.70.15142.166490.1514.05299.8
4.18-5011.60.08957.468240.0893.42498.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_473refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→42.815 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 0 / Phase error: 19.64 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 3021 4.97 %RANDOM
Rwork0.1585 ---
obs0.1609 60824 91.7 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.773 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 76.13 Å2 / Biso mean: 19.5496 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.0166 Å20 Å2-0 Å2
2--4.9185 Å20 Å2
3----2.9019 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7686 0 113 745 8544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077942
X-RAY DIFFRACTIONf_angle_d1.03410767
X-RAY DIFFRACTIONf_chiral_restr0.0721184
X-RAY DIFFRACTIONf_plane_restr0.0051427
X-RAY DIFFRACTIONf_dihedral_angle_d15.0993052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.9498-2.01950.26012540.177649535207520779
2.0195-2.10040.25022850.174354685753575388
2.1004-2.1960.22532910.16855455836583689
2.196-2.31170.22763080.166655985906590690
2.3117-2.45660.21692860.161757426028602892
2.4566-2.64620.21583080.161857906098609892
2.6462-2.91250.20963030.168258776180618093
2.9125-3.33380.21113230.166560526375637596
3.3338-4.19960.1723260.143162926618661899
4.1996-42.82550.18723370.14764866823682398

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