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- PDB-4eu7: Succinyl-CoA:acetate CoA-transferase (AarCH6) in complex with CoA... -

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Basic information

Entry
Database: PDB / ID: 4eu7
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6) 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: 1.7 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)114,15410
Polymers112,0932
Non-polymers2,0618
Water22,2671236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-74 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.415, 110.850, 120.373
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1236 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 M sodium citrate, 0.1 M imidazole, 25 mM 2-mercaptoethanol, and 2 mM CoA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 99312 / Num. obs: 99312 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Χ2: 1.231 / Net I/σ(I): 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.7-1.738.40.5422.948010.5420.82997.6
1.73-1.769.60.5463.448340.5460.8499.1
1.76-1.7910.60.5064.248970.5060.86799.6
1.79-1.8311.30.4645.149070.4640.86799.9
1.83-1.8711.90.4166.349600.4160.91100
1.87-1.9112.50.3687.848980.3680.951100
1.91-1.9613.10.3448.749420.3440.99599.9
1.96-2.0213.40.310.749160.31.059100
2.02-2.0713.90.26213.649440.2621.132100
2.07-2.1414.20.23115.849380.2311.171100
2.14-2.2214.30.19719.149460.1971.173100
2.22-2.3114.40.1742249800.1741.159100
2.31-2.4114.50.15324.549640.1531.174100
2.41-2.5414.70.13229.949530.1321.25100
2.54-2.714.80.12133.350040.1211.43100
2.7-2.9114.90.10340.749850.1031.546100
2.91-3.214.90.085250240.081.584100
3.2-3.6614.90.05671.450390.0561.638100
3.66-4.6114.70.04585.851020.0451.699100
4.61-5014.10.04285.352780.0421.57599.3

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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
Starting model: PDB ENTRY 2G39

2g39


Resolution: 1.7→28.8 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.16 / σ(F): 0 / Phase error: 18.09 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 4802 5.01 %RANDOM
Rwork0.1557 ---
obs0.1577 95944 96.26 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.934 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 75.07 Å2 / Biso mean: 18.7524 Å2 / Biso min: 4.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.0306 Å20 Å2-0 Å2
2--3.7377 Å20 Å2
3----3.7071 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 126 1236 9130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068135
X-RAY DIFFRACTIONf_angle_d1.04411048
X-RAY DIFFRACTIONf_chiral_restr0.0711212
X-RAY DIFFRACTIONf_plane_restr0.0051463
X-RAY DIFFRACTIONf_dihedral_angle_d14.9243167
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 (%)
1.7004-1.76120.26744430.223180468489848986
1.7612-1.83170.25964380.192186459083908392
1.8317-1.9150.21724720.163888679339933995
1.915-2.01590.22244740.158489929466946696
2.0159-2.14220.19534770.150191739650965097
2.1422-2.30750.20025060.152792399745974598
2.3075-2.53960.18124810.149293329813981399
2.5396-2.90680.20674900.159994499939993999
2.9068-3.66110.16825060.148895351004110041100
3.6611-28.80380.17385150.145398641037910379100

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