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- PDB-4euc: Succinyl-CoA:acetate CoA-transferase (AarCH6-E294A) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4euc
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6-E294A) in complex with dethiaacetyl-CoA
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
Chem-0RQ / Succinyl-CoA:acetate CoA-transferase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.644 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 1.2Jun 8, 2016Group: Other
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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)113,7018
Polymers111,9772
Non-polymers1,7256
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-75 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.490, 104.052, 120.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLYGLYchain A and (resseq 2:127 or resseq 129:199 or resseq...AA2 - 1272 - 127
12PHEPHEVALVALchain A and (resseq 2:127 or resseq 129:199 or resseq...AA129 - 199129 - 199
13ALAALAASPASPchain A and (resseq 2:127 or resseq 129:199 or resseq...AA201 - 236201 - 236
14THRTHRMETMETchain A and (resseq 2:127 or resseq 129:199 or resseq...AA238 - 309238 - 309
15ILEILEASNASNchain A and (resseq 2:127 or resseq 129:199 or resseq...AA311 - 329311 - 329
16METMETSERSERchain A and (resseq 2:127 or resseq 129:199 or resseq...AA331 - 505331 - 505
21THRTHRGLYGLYchain B and (resseq 2:127 or resseq 129:199 or resseq...BB2 - 1272 - 127
22PHEPHEVALVALchain B and (resseq 2:127 or resseq 129:199 or resseq...BB129 - 199129 - 199
23ALAALAASPASPchain B and (resseq 2:127 or resseq 129:199 or resseq...BB201 - 236201 - 236
24THRTHRMETMETchain B and (resseq 2:127 or resseq 129:199 or resseq...BB238 - 309238 - 309
25ILEILEASNASNchain B and (resseq 2:127 or resseq 129:199 or resseq...BB311 - 329311 - 329
26METMETSERSERchain B and (resseq 2:127 or resseq 129:199 or resseq...BB331 - 505331 - 505

NCS ensembles :
ID
1
2

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Components

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


Mass: 55988.254 Da / Num. of mol.: 2 / Mutation: E294A
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-0RQ / [[(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-(4-oxidanylidenepentylamino)propyl]amino]butyl] hydrogen phosphate / dethiaacetyl-coenzyme A


Mass: 791.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40N7O17P3
#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.: 205 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
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 10 mM dethiaacetyl-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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.644→50 Å / Num. all: 29835 / Num. obs: 29835 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Χ2: 1.416 / Net I/σ(I): 33.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.65-2.714.90.7546.214410.7540.982100
2.7-2.7414.80.6387.615040.6381.03100
2.74-2.814.90.5997.914210.5991.034100
2.8-2.8514.90.5159.414980.5151.056100
2.85-2.9214.90.4341214670.4341.129100
2.92-2.9814.90.38513.114630.3851.13100
2.98-3.0614.90.3611414800.3611.138100
3.06-3.1414.90.31516.614510.3151.199100
3.14-3.2314.90.23920.914800.2391.267100
3.23-3.3414.90.2124.614890.211.355100
3.34-3.4614.90.18226.414850.1821.425100
3.46-3.614.90.15133.414670.1511.606100
3.6-3.7614.90.13336.414910.1331.66100
3.76-3.9614.80.11842.514980.1181.718100
3.96-4.2114.70.10445.714890.1041.827100
4.21-4.5314.60.09152.115140.0911.897100
4.53-4.9914.60.08452.115060.0841.811100
4.99-5.7114.50.08349.815180.0831.506100
5.71-7.1914.30.07749.815350.0771.465100
7.19-5012.90.06760.916380.0672.10799.7

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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: 2.644→43.531 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.63 / σ(F): 0 / Phase error: 22.68 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1489 5 %RANDOM
Rwork0.1679 ---
obs0.1709 29775 99.93 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.053 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 114.82 Å2 / Biso mean: 46.5757 Å2 / Biso min: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1-6.008 Å20 Å2-0 Å2
2--7.7252 Å20 Å2
3----13.7332 Å2
Refinement stepCycle: LAST / Resolution: 2.644→43.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7676 0 106 205 7987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097930
X-RAY DIFFRACTIONf_angle_d1.06610744
X-RAY DIFFRACTIONf_chiral_restr0.0711174
X-RAY DIFFRACTIONf_plane_restr0.0051422
X-RAY DIFFRACTIONf_dihedral_angle_d13.1873028
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3787X-RAY DIFFRACTIONPOSITIONAL0.045
12B3787X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.6443-2.72960.29661330.2221253026632663
2.7296-2.82710.2751320.2134251026422642
2.8271-2.94030.30171340.2013254726812681
2.9403-3.07410.25961330.1959253826712671
3.0741-3.23610.27991340.1878253026642664
3.2361-3.43880.25891340.1848256426982698
3.4388-3.70420.23861350.1769254626812681
3.7042-4.07670.21641350.1562258127162716
4.0767-4.6660.1711370.1368259427312731
4.666-5.87640.19771380.1531261427522752
5.8764-43.53710.19741440.1515273228762876

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