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- PDB-1ooy: SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART -

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Basic information

Entry
Database: PDB / ID: 1ooy
TitleSUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
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 metabolic process / ketone body catabolic process / Mitochondrial protein degradation / protein homodimerization activity / mitochondrion
Similarity search - Function
3-oxoacid CoA-transferase / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / 3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / 3-oxoacid CoA-transferase, subunit B / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I ...3-oxoacid CoA-transferase / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / 3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / 3-oxoacid CoA-transferase, subunit B / 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
: / PHOSPHATE ION / Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCoros, A.M. / Swenson, L. / Wolodko, W.T. / Fraser, M.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the CoA transferase from pig heart to 1.7 A resolution.
Authors: Coros, A.M. / Swenson, L. / Wolodko, W.T. / Fraser, M.E.
History
DepositionMar 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8397
Polymers104,5882
Non-polymers2515
Water17,565975
1
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
hetero molecules

A: Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,67914
Polymers209,1764
Non-polymers50310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-21 kcal/mol
Surface area32850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.449, 140.325, 68.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1510-

HOH

DetailsThe biological assembly is a tetramer, generated by the two-fold axis: -x, -y,z.

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Components

#1: Protein Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor / Succinyl CoA:3-oxoacid CoA-transferase


Mass: 52293.957 Da / Num. of mol.: 2 / Fragment: succinyl-CoA:3-ketoacid CoA transferase monomer
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: OXCT OR SCOT / 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: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / 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: 2.06 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000, sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Jul 10, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 111125 / Num. obs: 100807 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.6
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.5 / % possible all: 73.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M3E

1m3e


Resolution: 1.7→19.81 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 9717 10.1 %RANDOM
Rwork0.156 ---
all0.175 105361 --
obs0.156 96525 91.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4975 Å2 / ksol: 0.359214 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---1.57 Å20 Å2
3---0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7098 0 9 975 8082
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 1403 10.3 %
Rwork0.198 12167 -
obs--78.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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