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

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Basic information

Entry
Database: PDB / ID: 1ooz
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: 2.1 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 1.3Aug 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

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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)103,2445
Polymers103,1262
Non-polymers1173
Water14,088782
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)206,48710
Polymers206,2534
Non-polymers2356
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 area5500 Å2
ΔGint-14 kcal/mol
Surface area33130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.819, 139.112, 68.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer, generated by the two-fold axis: 1-x, -y,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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.1 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 2000, sodium/potassium phosphate, sodium azide , pH 7.6, 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: Feb 24, 1999
RadiationMonochromator: GE 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→200 Å / Num. all: 57628 / Num. obs: 53376 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 40.1
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 9.2 / % possible all: 48.3

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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: 2.1→39.73 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 5219 10 %RANDOM
Rwork0.161 ---
all0.166 54747 --
obs0.161 51992 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8582 Å2 / ksol: 0.371032 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--1.85 Å20 Å2
3----1.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7057 0 3 782 7842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.272.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.205 726 9.7 %
Rwork0.152 6780 -
obs--83.7 %
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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