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- PDB-1ope: Deletion mutant of SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM P... -

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Basic information

Entry
Database: PDB / ID: 1ope
TitleDeletion mutant of SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 5, 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 1.3Aug 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_ref_seq_dif / 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.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_ref_seq_dif.details / _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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0078
Polymers103,1262
Non-polymers8816
Water3,639202
1
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase
hetero molecules

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)208,01416
Polymers206,2534
Non-polymers1,76112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-54 kcal/mol
Surface area33140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.640, 68.700, 103.500
Angle α, β, γ (deg.)90.00, 99.58, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer, generated by the two-fold axis: -x, y, -1-z.

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Components

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


Mass: 51563.152 Da / Num. of mol.: 2 / Mutation: 288-293 deletions
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: OXCT OR 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: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.57 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000, sodium/potassium phosphate, sodium azide , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 1999
RadiationMonochromator: GE 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 36137 / Num. obs: 30903 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 11.1 / % possible all: 86.2

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Processing

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

1ooy


Resolution: 2.5→38.13 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3093 10.1 %RANDOM
Rwork0.18 ---
all0.186 35673 --
obs0.18 30523 85.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.9358 Å2 / ksol: 0.334069 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.16 Å20 Å23.89 Å2
2---5.65 Å20 Å2
3----0.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6994 0 6 202 7202
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_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.012.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 526 -
Rwork0.2 0 -
obs-5176 87.6 %
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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