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- PDB-2nrc: C28A Mutant of Succinyl-CoA:3-Ketoacid CoA Transferase from Pig Heart -

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Basic information

Entry
Database: PDB / ID: 2nrc
TitleC28A Mutant of Succinyl-CoA:3-Ketoacid CoA Transferase from Pig Heart
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase 1
KeywordsTRANSFERASE / ALPHA/BETA PROTEIN
Function / homology
Function and homology information


Utilization of Ketone Bodies / cellular ketone body metabolic process / 3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone body catabolic process / Mitochondrial protein degradation / protein homodimerization activity / mitochondrion
Similarity search - Function
3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / 3-oxoacid CoA-transferase, subunit B / 3-oxoacid CoA-transferase / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I ...3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / 3-oxoacid CoA-transferase, subunit B / 3-oxoacid CoA-transferase / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsTammam, S.D. / Fraser, M.E.
CitationJournal: Biochemistry / Year: 2007
Title: Identification of the Cysteine Residue Exposed by the Conformational Change in Pig Heart Succinyl-CoA:3-Ketoacid Coenzyme A Transferase on Binding Coenzyme A.
Authors: Tammam, S.D. / Rochet, J.C. / Fraser, M.E.
History
DepositionNov 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1


Theoretical massNumber of molelcules
Total (without water)209,0484
Polymers209,0484
Non-polymers00
Water5,116284
1
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1


Theoretical massNumber of molelcules
Total (without water)104,5242
Polymers104,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-11 kcal/mol
Surface area34330 Å2
MethodPISA
2
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1


Theoretical massNumber of molelcules
Total (without water)104,5242
Polymers104,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-12 kcal/mol
Surface area34120 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.300, 262.400, 60.700
Angle α, β, γ (deg.)90.00, 109.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Succinyl-CoA:3-ketoacid-coenzyme A transferase 1 / Somatic-type succinyl CoA:3-oxoacid CoA- transferase / Scot-S


Mass: 52261.895 Da / Num. of mol.: 4 / Mutation: C28A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: OXCT1, OXCT, SCOT / Organ: Heart / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q29551, 3-oxoacid CoA-transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 2000, Tris-HCl, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.07
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2003
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.05→47.9 Å / Num. all: 95166 / Num. obs: 95166 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3128 / % possible all: 60.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
XFITdata reduction
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: C28S mutant

Resolution: 2.05→47.9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 5413 -consistent with other data sets from this crystal form
Rwork0.231 ---
all0.233 95112 --
obs0.233 95112 88.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.5 Å20 Å216.371 Å2
2--8.619 Å20 Å2
3---1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.05→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14290 0 0 284 14574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2.06→2.15 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.336 391 -
Rwork0.345 --
obs-6138 45.9 %

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