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

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Basic information

Entry
Database: PDB / ID: 4eua
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6-R228E) in complex with CoA (anomalous dataset)
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: 2.398 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)113,7138
Polymers112,0362
Non-polymers1,6776
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-76 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.391, 110.484, 119.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31B
41B
51B
61B
71B
81B
91B
101B
111B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISHISchain AAA2 - 5142 - 514
2SERSERchain B and ((resi 2:17))BB2 - 5052 - 505
3SERSERchain B and ((resi 19:49))BB2 - 5052 - 505
4SERSERchain B and ((resi 51:57))BB2 - 5052 - 505
5SERSERchain B and ((resi 59:199))BB2 - 5052 - 505
6SERSERchain B and ((resi 201:229))BB2 - 5052 - 505
7SERSERchain B and ((resi 235:308))BB2 - 5052 - 505
8SERSERchain B and ((resi 310:321))BB2 - 5052 - 505
9SERSERchain B and ((resi 323:410))BB2 - 5052 - 505
10SERSERchain B and ((resi 412:450))BB2 - 5052 - 505
11SERSERchain B and ((resi 452:505))BB2 - 5052 - 505

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 1.98 Å3/Da / Density % sol: 37.87 %
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-D / Wavelength: 1.9075 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9075 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. all: 34893 / Num. obs: 34893 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Χ2: 4.454 / Net I/σ(I): 54.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.4-2.495.70.10933.534770.1093.844100
2.49-2.595.70.09936.435000.0993.81799.8
2.59-2.75.70.0939.934890.093.98299.7
2.7-2.855.70.0854334800.0854.24299.5
2.85-3.025.70.07648.134940.0764.54599.4
3.02-3.265.70.06953.435000.0694.89298.9
3.26-3.585.70.0659.534820.065.06998.4
3.58-4.15.80.05662.934730.0565.2697.5
4.1-5.1760.05165.934870.0514.85796.4
5.17-506.20.04864.435110.0484.03493

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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: 2.398→44.636 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.64 / σ(F): 0 / Phase error: 19.76 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 3330 5.08 %RANDOM
Rwork0.1522 ---
obs0.1551 -97.48 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.021 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 102.1 Å2 / Biso mean: 17.2142 Å2 / Biso min: 2.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.5041 Å20 Å2-0 Å2
2--5.2349 Å20 Å2
3----3.7308 Å2
Refinement stepCycle: LAST / Resolution: 2.398→44.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7764 0 100 500 8364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078014
X-RAY DIFFRACTIONf_angle_d1.02310865
X-RAY DIFFRACTIONf_chiral_restr0.0681194
X-RAY DIFFRACTIONf_plane_restr0.0051439
X-RAY DIFFRACTIONf_dihedral_angle_d15.1483058
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A125X-RAY DIFFRACTIONPOSITIONAL0.04
12B125X-RAY DIFFRACTIONPOSITIONAL0.04
13B218X-RAY DIFFRACTIONPOSITIONAL0.039
14B56X-RAY DIFFRACTIONPOSITIONAL0.04
15B1071X-RAY DIFFRACTIONPOSITIONAL0.054
16B223X-RAY DIFFRACTIONPOSITIONAL0.055
17B555X-RAY DIFFRACTIONPOSITIONAL0.049
18B85X-RAY DIFFRACTIONPOSITIONAL0.045
19B660X-RAY DIFFRACTIONPOSITIONAL0.044
110B293X-RAY DIFFRACTIONPOSITIONAL0.04
111B444X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.3984-2.43260.23641490.152524092558255893
2.4326-2.46890.24041730.1626082781278199
2.4689-2.50750.30171340.173926512785278599
2.5075-2.54860.24071180.1684269228102810100
2.5486-2.59250.27091300.1766267628062806100
2.5925-2.63970.26151370.160926522789278999
2.6397-2.69050.24631560.1651264628022802100
2.6905-2.74540.22051440.158126112755275599
2.7454-2.8050.19971460.165826292775277599
2.805-2.87030.241340.159626002734273499
2.8703-2.94210.23431430.165326942837283799
2.9421-3.02160.26641410.175125782719271998
3.0216-3.11050.2811300.180126252755275598
3.1105-3.21080.24231280.171726512779277998
3.2108-3.32560.22891440.157425882732273298
3.3256-3.45870.21211360.15225842720272097
3.4587-3.6160.20781370.154725922729272997
3.616-3.80660.18221360.143125772713271397
3.8066-4.04490.15661370.128125942731273197
4.0449-4.3570.15951490.119625052654265496
4.357-4.7950.14031180.112225932711271195
4.795-5.48770.14681400.123725132653265396
5.4877-6.90980.18151300.159625412671267195
6.9098-44.64380.17771400.16724672607260793

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