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- PDB-5ddk: Succinyl-CoA:acetate CoA-transferase (AarCH6-N347A) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5ddk
TitleSuccinyl-CoA:acetate CoA-transferase (AarCH6-N347A) in complex with CoA
ComponentsAcetyl-CoA hydrolase
KeywordsTRANSFERASE / Tricarboxylic acid cycle / Acidophile
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
COENZYME A / IMIDAZOLE / Acetyl-CoA hydrolase / Succinyl-CoA:acetate CoA-transferase
Similarity search - Component
Biological speciesAcetobacter aceti 1023 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.127 Å
AuthorsKappock, T.J. / Mullins, E.A. / Murphy, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB0936108 United States
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
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA hydrolase
B: Acetyl-CoA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,89111
Polymers112,0072
Non-polymers1,8849
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-57 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.103, 109.775, 120.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetyl-CoA hydrolase


Mass: 56003.266 Da / Num. of mol.: 2 / Mutation: N347A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti 1023 (bacteria) / Gene: AZ09_02565 / Plasmid: pET23a / Details (production host): pJK524 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: A0A063X8M7, UniProt: B3EY95*PLUS, 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: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 1.91 Å3/Da / Density meas: 35.7 Mg/m3 / Density % sol: 37.69 %
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, 2 mM coenzyme A

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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: Jun 27, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.127→50 Å / Num. obs: 50048 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rsym value: 0.116 / Net I/σ(I): 22.9
Reflection shellResolution: 2.127→2.17 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.652 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eu9

4eu9


Resolution: 2.127→32.337 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2394 5 %same as 4eu9
Rwork0.1449 ---
obs0.1473 47881 94.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.127→32.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7751 0 115 623 8489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048091
X-RAY DIFFRACTIONf_angle_d0.85910968
X-RAY DIFFRACTIONf_dihedral_angle_d12.8822990
X-RAY DIFFRACTIONf_chiral_restr0.0321202
X-RAY DIFFRACTIONf_plane_restr0.0041454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1274-2.17090.23231190.17062395X-RAY DIFFRACTION85
2.1709-2.21810.22191370.1672453X-RAY DIFFRACTION88
2.2181-2.26960.23221430.16772523X-RAY DIFFRACTION91
2.2696-2.32640.24811370.16192511X-RAY DIFFRACTION90
2.3264-2.38930.22621310.16442576X-RAY DIFFRACTION92
2.3893-2.45950.22321300.15932566X-RAY DIFFRACTION92
2.4595-2.53890.20891420.16372608X-RAY DIFFRACTION93
2.5389-2.62960.24711410.16212628X-RAY DIFFRACTION94
2.6296-2.73480.20371390.16582669X-RAY DIFFRACTION95
2.7348-2.85920.26781380.16862702X-RAY DIFFRACTION96
2.8592-3.00990.20981440.16612761X-RAY DIFFRACTION98
3.0099-3.19830.21031450.16152777X-RAY DIFFRACTION98
3.1983-3.4450.19091400.14262782X-RAY DIFFRACTION99
3.445-3.79120.18761570.12382809X-RAY DIFFRACTION99
3.7912-4.33870.13631460.11442843X-RAY DIFFRACTION100
4.3387-5.4620.14221490.11282897X-RAY DIFFRACTION100
5.462-32.34030.15371560.14042987X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.068-0.2008-0.1150.37170.09570.96710.00430.1122-0.0361-0.0596-0.0267-0.0811-0.0040.20880.01630.1142-0.00760.01640.19110.01180.169510.0321-5.73267.8331
21.0770.8753-1.01920.7318-0.71711.2633-0.1439-0.0257-0.60880.0154-0.11510.06060.22760.00660.27580.1788-0.03490.02280.2067-0.06930.2456-15.138-18.89716.337
32.41680.2749-1.05041.47820.16152.4576-0.2911-0.2277-0.588-0.044-0.056-0.11410.48180.02820.20020.21680.02180.05150.19650.02310.2808-13.0911-14.60745.7513
40.4907-0.22490.08090.64780.18491.5213-0.0257-0.04-0.0860.0867-0.0130.0910.0445-0.16130.03560.0979-0.01510.01870.1152-0.00850.1657-16.6131-5.984529.0879
51.564-0.97690.3181.4530.63511.2073-0.0958-0.2865-0.18230.23760.06090.0980.206-0.2135-0.03280.22150.00190.03680.22410.05430.1761-13.2708-7.386846.4154
61.0252-0.12490.47970.7143-0.38650.9251-0.1172-0.18850.0961-0.04290.00010.1547-0.4326-0.6081-0.00960.29680.186-0.05120.3764-0.06550.2247-35.54319.406323.3749
70.9617-0.46650.12131.25590.23860.1291-0.00230.04540.1107-0.3993-0.10790.0208-0.5126-0.23750.03060.36720.1248-0.07530.2728-0.01120.1663-27.868819.19146.7532
81.30550.39331.33230.6886-0.03991.7012-0.1361-0.40570.1403-0.03-0.09550.0679-0.3859-0.01360.23990.3421-0.0494-0.02870.1089-0.02010.238-6.630728.744226.7766
90.4609-0.05560.23360.4580.02850.7281-0.03390.00540.1458-0.1057-0.0035-0.0414-0.3064-0.05350.02230.25990.0008-0.00280.11920.0040.1934-8.893721.361122.6168
100.88280.52920.8981.99011.38243.8431-0.0238-0.0663-0.00080.00040.0382-0.1789-0.24970.2073-0.00360.1268-0.0434-0.00590.1826-0.00120.20346.44348.937439.3907
111.8577-2.5788-2.54954.74663.31044.2246-0.1849-0.2231-0.07030.35690.2372-0.05050.08990.3254-0.14570.1316-0.0371-0.04030.19070.01410.1319-3.17274.862845.3634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 223 )
2X-RAY DIFFRACTION2chain 'A' and (resid 224 through 255 )
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 348 )
4X-RAY DIFFRACTION4chain 'A' and (resid 349 through 476 )
5X-RAY DIFFRACTION5chain 'A' and (resid 477 through 513 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 176 )
7X-RAY DIFFRACTION7chain 'B' and (resid 177 through 223 )
8X-RAY DIFFRACTION8chain 'B' and (resid 224 through 255 )
9X-RAY DIFFRACTION9chain 'B' and (resid 256 through 445 )
10X-RAY DIFFRACTION10chain 'B' and (resid 446 through 476 )
11X-RAY DIFFRACTION11chain 'B' and (resid 477 through 505 )

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