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- PDB-4eu3: Succinyl-CoA:acetate CoA-transferase (AarCH6) in complex with cit... -

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Basic information

Entry
Database: PDB / ID: 4eu3
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6) in complex with citrate (subunit B) or unliganded (subunit A)
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 / Succinyl-CoA:acetate CoA-transferase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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

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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)112,4277
Polymers112,0932
Non-polymers3345
Water22,9151272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-73 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.478, 110.347, 119.837
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 1272 / 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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.9 M sodium citrate, 0.1 M imidazole, and 25 mM 2-mercaptoethanol, 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: Mar 15, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 121024 / Num. obs: 121024 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Χ2: 0.851 / Net I/σ(I): 21.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.58-1.614.90.4422.152110.4420.66886
1.61-1.645.80.432.555310.430.66390.8
1.64-1.676.80.4372.957150.4370.65494.2
1.67-1.78.10.4173.559160.4170.6797.1
1.7-1.749.50.4014.460310.4010.66699.1
1.74-1.7811.10.4085.161330.4080.67999.9
1.78-1.8212.50.3826.560690.3820.708100
1.82-1.8713.30.3377.961480.3370.728100
1.87-1.9313.70.28210.160540.2820.731100
1.93-1.99140.23811.561220.2380.745100
1.99-2.0614.10.1914.461090.190.749100
2.06-2.1414.20.1617.261160.160.777100
2.14-2.2414.40.13820.961330.1380.774100
2.24-2.3614.60.12422.661470.1240.795100
2.36-2.5114.80.10827.561800.1080.828100
2.51-2.714.90.10231.561560.1020.984100
2.7-2.97150.09237.761900.0921.264100
2.97-3.4150.07449.762380.0741.444100
3.4-4.2914.80.04269.662850.0420.997100
4.29-5014.20.03276.165400.0320.802100

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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: 1.58→40.234 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.43 / σ(F): 0 / Phase error: 17.14 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 6055 5.01 %RANDOM
Rwork0.1557 ---
obs0.1573 120904 98.3 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.801 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 76.15 Å2 / Biso mean: 14.3122 Å2 / Biso min: 3.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.2324 Å20 Å2-0 Å2
2--4.0437 Å20 Å2
3----1.8113 Å2
Refinement stepCycle: LAST / Resolution: 1.58→40.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 17 1272 9057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067990
X-RAY DIFFRACTIONf_angle_d1.06810831
X-RAY DIFFRACTIONf_chiral_restr0.0741195
X-RAY DIFFRACTIONf_plane_restr0.0051449
X-RAY DIFFRACTIONf_dihedral_angle_d12.5073009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.5796-1.59760.29831960.257832023398339884
1.5976-1.61630.29041730.266134213594359488
1.6163-1.63610.26161890.227834943683368391
1.6361-1.65680.22971750.213536223797379793
1.6568-1.67860.25061910.203837043895389596
1.6786-1.70160.22622130.182337243937393798
1.7016-1.72590.20721990.173838214020402099
1.7259-1.75160.20822100.167383240424042100
1.7516-1.7790.17622040.1616389340974097100
1.779-1.80820.22311970.1625384940464046100
1.8082-1.83940.21232040.1569386340674067100
1.8394-1.87280.20941960.1578390140974097100
1.8728-1.90880.20091980.1545381940174017100
1.9088-1.94780.20632000.1582385340534053100
1.9478-1.99010.20772070.154390541124112100
1.9901-2.03640.19192060.152385240584058100
2.0364-2.08730.17651940.1536387740714071100
2.0873-2.14380.18472100.1485389141014101100
2.1438-2.20690.17742100.1522389741074107100
2.2069-2.27810.18952080.1533385140594059100
2.2781-2.35950.18262150.1559390141164116100
2.3595-2.4540.1841880.1472392141094109100
2.454-2.56560.20712070.1528388340904090100
2.5656-2.70090.1832110.1576391641274127100
2.7009-2.870.18511970.1622391741144114100
2.87-3.09160.19582030.1566395041534153100
3.0916-3.40250.15492120.1467394741594159100
3.4025-3.89450.15642140.1264395741714171100
3.8945-4.90530.14982040.1231402742314231100
4.9053-40.24680.18052240.1567415943834383100

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