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- PDB-1m3e: Succinyl-COA:3-ketoacid COA transferase from pig heart (selenomet... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1m3e
TitleSuccinyl-COA:3-ketoacid COA transferase from pig heart (selenomethionine)
ComponentsSUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE
KeywordsTRANSFERASE / alpha/beta protein
Function / homology
Function and homology information


Utilization of Ketone Bodies / : / 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 / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / 3-oxoacid CoA-transferase, subunit B / 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 / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / 3-oxoacid CoA-transferase, subunit B / 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 / MAD / Resolution: 2.5 Å
AuthorsBateman, K.S. / Brownie, E.R. / Wolodko, W.T. / Fraser, M.E.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of the Mammalian CoA Transferase from Pig Heart
Authors: Bateman, K.S. / Brownie, E.R. / Wolodko, W.T. / Fraser, M.E.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE
B: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE
C: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE
D: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)211,6144
Polymers211,6144
Non-polymers00
Water15,475859
1
A: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE
B: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)105,8072
Polymers105,8072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-14 kcal/mol
Surface area35200 Å2
MethodPISA
2
C: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE
D: SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)105,8072
Polymers105,8072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-15 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.168, 264.323, 62.688
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE / SUCCINYL COA:3-OXOACID COA-TRANSFERASE


Mass: 52903.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: heart / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q29551, 3-oxoacid CoA-transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 2000, TrisCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %(w/v)PEG20001reservoir
2100 mMTris-Cl1reservoirpH8.0
30.125-0.5 M1dropKCl
422.8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.978,0.979,0.961
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.9791
30.9611
ReflectionResolution: 2.5→30 Å / Num. all: 62373 / Num. obs: 61401 / % possible obs: 97.9 % / Redundancy: 6.75 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 27.42
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 6.99 / % possible all: 84.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 414407
Reflection shell
*PLUS
% possible obs: 84.3 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3199 -shells
Rwork0.221 ---
all0.246 62373 --
obs0.246 60288 96.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14441 0 0 859 15300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_mcangle_it2.926
X-RAY DIFFRACTIONc_mcbond_it1.821
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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