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- PDB-5e5h: Succinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate an... -

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Basic information

Entry
Database: PDB / ID: 5e5h
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6) bound to acetate and degradation products from the acetyl-CoA analogue dethiaacetyl-CoA
ComponentsSuccinyl-CoA:acetate CoA-transferase
KeywordsTRANSFERASE / Tricarboxylic acid cycle / Acidophile / coenzyme analogue
Function / homology
Function and homology information


succinyl-CoA:acetate CoA-transferase / acetate catabolic process / propionate metabolic process, methylcitrate cycle / acetyl-CoA hydrolase activity / acetate CoA-transferase activity / succinyl-CoA catabolic process / acetate metabolic process / acetyl-CoA biosynthetic process from acetate / acetyl-CoA metabolic process / transferase activity
Similarity search - Function
Succinate CoA transferase / Acetyl-CoA hydrolase/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 N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / NagB/RpiA transferase-like
Similarity search - Domain/homology
Chem-0T1 / ACETYL GROUP / ACETATE ION / FORMIC ACID / IMIDAZOLE / Acetyl-CoA hydrolase / Succinyl-CoA:acetate CoA-transferase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.052 Å
AuthorsMullins, E.A. / Kappock, T.J.
Citation
Journal: Front Chem / Year: 2016
Title: Functional Dissection of the Bipartite Active Site of the Class I Coenzyme A (CoA)-Transferase Succinyl-CoA:Acetate CoA-Transferase.
Authors: Murphy, J.R. / Mullins, E.A. / Kappock, T.J.
#1: 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.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMay 18, 2016ID: 4FAC
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinyl-CoA:acetate CoA-transferase
B: Succinyl-CoA:acetate CoA-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,19115
Polymers112,1252
Non-polymers2,06613
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-62 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.192, 109.844, 119.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Succinyl-CoA:acetate CoA-transferase


Mass: 56062.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Gene: AZ09_02565 / Plasmid: pET23a / Details (production host): pJK385 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0A063X8M7, UniProt: B3EY95*PLUS

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Non-polymers , 7 types, 611 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-0T1 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(propylamino)propyl]amino]butyl] hydrogen phosphate / DETHIACOENZYME A


Mass: 749.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H38N7O16P3
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.6 %
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, 10 mM dethiaacetyl-CoA

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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: 2.05→50 Å / Num. obs: 55051 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Rsym value: 0.125 / Net I/σ(I): 24.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.64 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4eu9
Resolution: 2.052→41.393 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2740 4.99 %same as 4fac
Rwork0.1511 ---
obs0.1533 54907 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.052→41.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7749 0 125 598 8472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138108
X-RAY DIFFRACTIONf_angle_d1.37610999
X-RAY DIFFRACTIONf_dihedral_angle_d13.9673015
X-RAY DIFFRACTIONf_chiral_restr0.0581212
X-RAY DIFFRACTIONf_plane_restr0.0081459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0521-2.08750.23791320.18022552X-RAY DIFFRACTION96
2.0875-2.12540.20841260.17182515X-RAY DIFFRACTION97
2.1254-2.16630.23191350.16752573X-RAY DIFFRACTION97
2.1663-2.21050.26031340.16272527X-RAY DIFFRACTION97
2.2105-2.25860.22341410.17152555X-RAY DIFFRACTION96
2.2586-2.31110.22081310.17552536X-RAY DIFFRACTION97
2.3111-2.36890.241360.16112553X-RAY DIFFRACTION97
2.3689-2.4330.22961250.15712542X-RAY DIFFRACTION97
2.433-2.50450.21491370.16042547X-RAY DIFFRACTION96
2.5045-2.58540.22891350.15932557X-RAY DIFFRACTION96
2.5854-2.67780.23051360.16592571X-RAY DIFFRACTION98
2.6778-2.78490.24581270.16772589X-RAY DIFFRACTION97
2.7849-2.91170.20811470.16442609X-RAY DIFFRACTION98
2.9117-3.06510.20051400.16812658X-RAY DIFFRACTION100
3.0651-3.25710.19461410.15792643X-RAY DIFFRACTION100
3.2571-3.50850.20241380.1482682X-RAY DIFFRACTION100
3.5085-3.86130.15771400.13022670X-RAY DIFFRACTION99
3.8613-4.41950.15191430.11692698X-RAY DIFFRACTION100
4.4195-5.56590.13951470.12752723X-RAY DIFFRACTION100
5.5659-41.40180.1611490.15012867X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.96910.37350.32480.2868-0.04460.7699-0.0091-0.13740.1620.0624-0.0362-0.0966-0.11950.32150.02920.1201-0.032-0.02910.2567-0.00010.20717.55899.9309-9.3236
21.04310.13820.02350.44730.05620.92960.0057-0.1870.00340.0719-0.0366-0.05270.01240.17850.02650.10050.0057-0.00990.14470.01260.14186.13793.9269-7.319
31.7279-0.7151.99260.3421-0.54232.4908-0.14840.12980.62380.0322-0.05250.0559-0.24740.12910.19290.16850.0359-0.02270.1605-0.0480.2382-15.333418.9716-16.5691
45.92851.64280.18665.8682-1.29524.0653-0.13210.22260.44080.0647-0.1501-0.0468-0.37270.00550.24980.14680.0143-0.05010.1658-0.00120.1419-20.944313.8814-12.3142
50.5255-0.1622-0.02540.1520.08372.1443-0.0185-0.05630.09070.0257-0.0035-0.0055-0.16230.01460.01770.1131-0.0137-0.01570.1050.00630.1643-11.43539.7469-15.0934
60.9970.1993-0.24770.95580.47930.8678-0.06170.2040.1263-0.1531-0.01510.0567-0.1033-0.15640.03630.13020.0094-0.04080.15870.04420.1397-18.96297.1713-40.5595
71.18370.1668-0.77150.5107-0.60811.1232-0.22650.3674-0.1496-0.00730.07550.16040.4994-0.7115-0.03250.2277-0.2350.06620.4167-0.08060.2064-35.9272-17.7282-25.9629
81.38940.5951-0.5121.11990.22910.86-0.218-0.0781-0.17620.2769-0.01170.12720.5199-0.33810.02860.3758-0.12950.10360.2469-0.01130.1817-30.4344-21.5017-9.7506
91.335-0.4654-1.06890.33030.13981.0779-0.52380.4368-0.62210.16810.14010.07150.7765-0.12340.19580.4130.05050.12050.07430.01050.3098-6.4725-29.077-26.5209
105.72870.8602-1.07592.7576-0.24441.6804-0.20130.4373-0.46680.27180.2195-0.0720.26840.1649-0.02930.34050.06170.01930.1454-0.00160.2069-3.5195-26.5961-17.4148
110.7729-0.0389-0.22610.43780.27660.6967-0.06750.0225-0.19040.1198-0.02240.02560.319-0.01460.01030.2327-0.0090.02980.0730.0050.1844-10.0601-20.1011-23.6642
121.39720.57970.71251.89690.54441.4971-0.04160.1649-0.0282-0.12480.0384-0.17270.02490.2093-0.01040.09220.00570.03770.14890.00880.12592.0235-7.0813-42.3438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 255 )
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 283 )
5X-RAY DIFFRACTION5chain 'A' and (resid 284 through 430 )
6X-RAY DIFFRACTION6chain 'A' and (resid 431 through 512 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 223 )
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 255 )
10X-RAY DIFFRACTION10chain 'B' and (resid 256 through 294 )
11X-RAY DIFFRACTION11chain 'B' and (resid 295 through 445 )
12X-RAY DIFFRACTION12chain 'B' and (resid 446 through 505 )

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