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- PDB-1o9l: Succinate:Coenzyme-A Transferase (pig heart) -

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Basic information

Entry
Database: PDB / ID: 1o9l
TitleSuccinate:Coenzyme-A Transferase (pig heart)
ComponentsSUCCINYL-COA\:3-KETOACID-COENZYME A TRANSFERASE
KeywordsTRANSFERASE / CONEZYME-A / MAD / PATHOGENIC MUTATIONS
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
ETHYL MERCURY ION / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID / Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsMitchell, E.P. / Lloyd, A.J. / Lewis, G. / Shoolingin-Jordan, P.
CitationJournal: To be Published
Title: Succinate:Coenzyme-A Transferase Deficiency: A Structural View of Pathogenic Mutations
Authors: Mitchell, E.P. / Lloyd, A.J. / Lewis, G. / Shoolingin-Jordan, P.
History
DepositionDec 17, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,54913
Polymers209,1764
Non-polymers2,3739
Water9,224512
1
A: SUCCINYL-COA\:3-KETOACID-COENZYME A TRANSFERASE
B: SUCCINYL-COA\:3-KETOACID-COENZYME A TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8136
Polymers104,5882
Non-polymers1,2254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SUCCINYL-COA\:3-KETOACID-COENZYME A TRANSFERASE
D: SUCCINYL-COA\:3-KETOACID-COENZYME A TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7367
Polymers104,5882
Non-polymers1,1485
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.800, 133.800, 101.900
Angle α, β, γ (deg.)90.00, 104.40, 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 / OXCT / SCOT


Mass: 52293.957 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: HEART / References: UniProt: Q29551, 3-oxoacid CoA-transferase
#2: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Chemical ChemComp-EMT / 2-(ETHYLMERCURI-THIO)-BENZOIC ACID


Mass: 382.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10HgO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Compound detailsKEY ENZYME FOR KETONE BODY CATABOLISM. TRANSFERS THE COA MOIETY FROM SUCCINATE TO ACETOACETATE. ...KEY ENZYME FOR KETONE BODY CATABOLISM. TRANSFERS THE COA MOIETY FROM SUCCINATE TO ACETOACETATE. FORMATION OF THE ENZYME-COA INTERMEDIATE PROCEEDS VIA AN UNSTABLE ANHYDRIDE SPECIES FORMED BETWEEN THE CARBOXYLATE GROUPS OF THE ENZYME AND SUBSTRATE.

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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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.008,0.8300
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: TOROIDAL MIRROR
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
20.831
ReflectionResolution: 2.4→30 Å / Num. obs: 73890 / % possible obs: 94.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 39.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.27 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2143399.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES IN THE SERVERAL REGIONS WERE NOT VISIBLE IN ELECTRON DENSITY MAPS AND WERE NOT MODELLED: A/B287-299,C286-299, D283-299, B/C401-419, B/C441-465
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1506 2 %RANDOM
Rwork0.24 ---
obs0.24 75611 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.1123 Å2 / ksol: 0.377739 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.97 Å20 Å22.08 Å2
2---8.26 Å20 Å2
3----1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-30 Å
Luzzati sigma a0.33 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13576 0 47 512 14135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
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_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 230 1.8 %
Rwork0.277 12313 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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