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- PDB-4eu9: Succinyl-CoA:acetate CoA-transferase (AarCH6-R228E) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4eu9
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6-R228E) in complex with CoA and a covalent glutamyl-CoA thioester adduct
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: 1.479 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 1.3Oct 30, 2024Group: 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)113,7138
Polymers112,0362
Non-polymers1,6776
Water23,8881326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-67 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.093, 110.099, 119.841
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: 56018.211 Da / Num. of mol.: 2 / Mutation: R228E
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.: 1326 / 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: 37.73 %
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 succinyl-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: 1.479→50 Å / Num. all: 148137 / Num. obs: 148137 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Χ2: 1.178 / Net I/σ(I): 38.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.48-1.5112.90.5744.473180.5740.68899.8
1.51-1.5312.90.55.172810.50.73799.8
1.53-1.56130.428673860.4280.71699.9
1.56-1.5913.10.372772960.3720.719100
1.59-1.6313.10.3337.773560.3330.72599.9
1.63-1.6713.10.2988.873000.2980.73699.9
1.67-1.7113.20.25710.173360.2570.75499.9
1.71-1.7513.20.22911.773600.2290.781100
1.75-1.8113.30.19813.573750.1980.78799.9
1.81-1.8613.40.16616.373720.1660.826100
1.86-1.9313.50.14620.473840.1460.939100
1.93-2.0113.60.11625.773570.1160.963100
2.01-2.113.70.10931.373850.1091.219100
2.1-2.2113.90.10436.973930.1041.594100
2.21-2.3513.80.10440.974440.1042.007100
2.35-2.5313.90.09647.974060.0962.263100
2.53-2.7914.20.08655.374880.0862.276100
2.79-3.1914.70.05467.575090.0541.566100
3.19-4.0214.80.03787.275580.0371.478100
4.02-5014.10.03290.478330.0321.35799.7

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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: 1.479→30.998 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.14 / σ(F): 0 / Phase error: 17.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 7386 4.99 %RANDOM
Rwork0.1574 ---
obs0.1585 147934 99.83 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.035 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 67.11 Å2 / Biso mean: 15.2522 Å2 / Biso min: 4.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.2319 Å20 Å2-0 Å2
2--3.8218 Å20 Å2
3----2.5899 Å2
Refinement stepCycle: LAST / Resolution: 1.479→30.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7764 0 100 1326 9190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068137
X-RAY DIFFRACTIONf_angle_d1.14311064
X-RAY DIFFRACTIONf_chiral_restr0.0751221
X-RAY DIFFRACTIONf_plane_restr0.0061465
X-RAY DIFFRACTIONf_dihedral_angle_d14.8573143
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 (%)
1.4795-1.49630.22132320.191445964828482898
1.4963-1.51390.24942510.1887457748284828100
1.5139-1.53240.22182520.1783464949014901100
1.5324-1.55180.19522540.1711464548994899100
1.5518-1.57220.20552250.1678464848734873100
1.5722-1.59370.19262340.167466348974897100
1.5937-1.61650.19772480.16463348814881100
1.6165-1.64060.19972380.1594466349014901100
1.6406-1.66620.20082360.1624463348694869100
1.6662-1.69360.19522620.1604468449464946100
1.6936-1.72280.17572220.1535464948714871100
1.7228-1.75410.20692700.158460748774877100
1.7541-1.78780.20382540.1579465749114911100
1.7878-1.82430.19732180.1629468849064906100
1.8243-1.8640.19062570.1602468149384938100
1.864-1.90730.16882390.1524465848974897100
1.9073-1.9550.18722610.1572463548964896100
1.955-2.00790.18252360.1592468549214921100
2.0079-2.06690.18132530.1592467449274927100
2.0669-2.13360.17892310.1552467249034903100
2.1336-2.20990.17422580.1518466649244924100
2.2099-2.29830.17572450.1583470049454945100
2.2983-2.40290.19872520.1609470049524952100
2.4029-2.52950.18972400.161468349234923100
2.5295-2.68790.19342490.1731473649854985100
2.6879-2.89530.20752470.1692473749844984100
2.8953-3.18640.18682540.1651474349974997100
3.1864-3.64690.13662500.1427476750175017100
3.6469-4.59230.13862500.1292482350735073100
4.5923-31.00470.16222680.1602499652645264100

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