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Basic information

Entry
Database: PDB / ID: 2ib9
TitleCrystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase (T2): the importance of potassium and chloride for its structure and function
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase fold / potassium ion / chloride / beta-alpha-beta-alpha-beta-alpha-beta-beta topology / alpha-beta-alpha-beta-alpha layered structure
Function / homology
Function and homology information


C-acetyltransferase activity / metanephric proximal convoluted tubule development / propionyl-CoA biosynthetic process / Beta-ketothiolase deficiency / Utilization of Ketone Bodies / Synthesis of Ketone Bodies / cholesterol O-acyltransferase activity / ketone body metabolic process / ketone body catabolic process / acetyl-CoA catabolic process ...C-acetyltransferase activity / metanephric proximal convoluted tubule development / propionyl-CoA biosynthetic process / Beta-ketothiolase deficiency / Utilization of Ketone Bodies / Synthesis of Ketone Bodies / cholesterol O-acyltransferase activity / ketone body metabolic process / ketone body catabolic process / acetyl-CoA catabolic process / acetyl-CoA C-acetyltransferase / L-isoleucine catabolic process / coenzyme A binding / Maturation of TCA enzymes and regulation of TCA cycle / acetyl-CoA C-acetyltransferase activity / acetyl-CoA biosynthetic process / Branched-chain amino acid catabolism / coenzyme A metabolic process / coenzyme A biosynthetic process / response to starvation / fatty acid beta-oxidation / potassium ion binding / adipose tissue development / response to hormone / Mitochondrial protein degradation / liver development / mitochondrial matrix / enzyme binding / endoplasmic reticulum / mitochondrion / extracellular exosome / identical protein binding
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Acetyl-CoA acetyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHaapalainen, A.M. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2007
Title: Crystallographic and Kinetic Studies of Human Mitochondrial Acetoacetyl-CoA Thiolase: The Importance of Potassium and Chloride Ions for Its Structure and Function
Authors: Haapalainen, A.M. / Merilainen, G. / Pirila, P.L. / Kondo, N. / Fukao, T. / Wierenga, R.K.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,67221
Polymers166,1324
Non-polymers1,54017
Water16,898938
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18280 Å2
ΔGint-117 kcal/mol
Surface area52370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.749, 107.440, 102.326
Angle α, β, γ (deg.)90.00, 103.06, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit consists of one biological unit, the homotetramer

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase / T2


Mass: 41533.047 Da / Num. of mol.: 4 / Mutation: V34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: liver / Gene: ACAT1 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P24752, acetyl-CoA C-acetyltransferase

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Non-polymers , 5 types, 955 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 938 / 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: 2.44 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 5000 monomethylether, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.4022 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2006 / Details: mirrors
RadiationMonochromator: Fixed exit double crystal Si [111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4022 Å / Relative weight: 1
ReflectionResolution: 2.05→73.72 Å / Num. all: 100031 / Num. obs: 99949 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 16.3
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.9 / Num. unique all: 13221 / Rsym value: 0.357 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WL4

1wl4


Resolution: 2.05→73.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.727 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.174 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 4998 5 %RANDOM
Rwork0.15601 ---
obs0.15817 94953 100 %-
all-99951 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.34 Å2
2--0.34 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.05→73.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11512 0 86 938 12536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211875
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.98616079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60451563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62125.941404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.491152131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.351536
X-RAY DIFFRACTIONr_chiral_restr0.0880.21931
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028532
X-RAY DIFFRACTIONr_nbd_refined0.2020.25406
X-RAY DIFFRACTIONr_nbtor_refined0.2910.28199
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2818
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.217
X-RAY DIFFRACTIONr_mcbond_it1.30237788
X-RAY DIFFRACTIONr_mcangle_it1.956412552
X-RAY DIFFRACTIONr_scbond_it1.51934123
X-RAY DIFFRACTIONr_scangle_it2.14243527
LS refinement shellResolution: 2.05→2.122 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.26 487 -
Rwork0.197 9254 -
obs-9254 100 %

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