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- PDB-4eu4: Succinyl-CoA: acetate CoA-transferase (AarCH6) in complex with Co... -

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Basic information

Entry
Database: PDB / ID: 4eu4
TitleSuccinyl-CoA: acetate CoA-transferase (AarCH6) in complex with CoA (hexagonal lattice)
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: 2.802 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)115,69128
Polymers112,0932
Non-polymers3,59826
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-248 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.180, 150.180, 290.393
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 2 - 505 / Label seq-ID: 2 - 505

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 2:505 )AA
2chain B and (resseq 2:505 )BB

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#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.: 295 / 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: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M ammonium sulfate, 0.1 M sodium cacodylate, 0.2 M sodium chloride, 25 mM 2-mercaptoethanol, and 2 mM CoA, pH 6.5, 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: Oct 9, 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: 2.8→50 Å / Num. all: 46836 / Num. obs: 46836 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 18 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Χ2: 1.596 / 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
2.8-2.8512.50.7183.921730.7181.04692.2
2.85-2.9140.5865.121910.5861.08493.2
2.9-2.9615.30.5665.522490.5661.195.1
2.96-3.0216.90.5146.722710.5141.06995.7
3.02-3.0817.60.4757.722460.4751.09695.5
3.08-3.1517.80.3929.222540.3921.0995.5
3.15-3.2317.90.29812.722750.2981.21295.8
3.23-3.3217.90.25415.522470.2541.23494.7
3.32-3.4217.90.2261822830.2261.32894.5
3.42-3.5317.70.19122.922610.1911.59196.4
3.53-3.6517.60.1622722900.1621.67795.4
3.65-3.817.50.1363323330.1361.86197.7
3.8-3.9717.30.11937.123950.1191.93399.2
3.97-4.1817.60.09845.124090.0981.88599.9
4.18-4.4418.30.0815923960.0812.084100
4.44-4.7919.10.07865.424280.0782.235100
4.79-5.2720.50.0766924490.0762.302100
5.27-6.0322.10.07171.624740.0711.865100
6.03-7.5922.90.05286.225130.0521.624100
7.59-5020.50.036101.526990.0361.68399.9

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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: 2.802→41.541 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.32 / σ(F): 0 / Phase error: 21.58 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 2273 5.06 %RANDOM
Rwork0.1779 ---
obs0.1801 44896 92.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.666 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 147.43 Å2 / Biso mean: 49.7383 Å2 / Biso min: 17.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.1712 Å20 Å2-0 Å2
2--2.1712 Å20 Å2
3----4.3423 Å2
Refinement stepCycle: LAST / Resolution: 2.802→41.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7684 0 200 295 8179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088008
X-RAY DIFFRACTIONf_angle_d1.20110866
X-RAY DIFFRACTIONf_chiral_restr0.0721184
X-RAY DIFFRACTIONf_plane_restr0.0061422
X-RAY DIFFRACTIONf_dihedral_angle_d17.6063034
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3842X-RAY DIFFRACTIONPOSITIONAL0.041
12B3842X-RAY DIFFRACTIONPOSITIONAL0.041
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 (%)
2.802-2.90210.35922010.286636223823382381
2.9021-3.01830.31352140.251239314145414587
3.0183-3.15560.31792110.255340234234423489
3.1556-3.32190.30862210.227140984319431991
3.3219-3.530.23992200.200141564376437692
3.53-3.80230.21542300.173242714501450194
3.8023-4.18470.20612370.157544864723472398
4.1847-4.78940.17422410.132645734814481499
4.7894-6.03120.19242470.1533466149084908100
6.0312-41.54560.1832510.160148025053505397

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