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- PDB-2ibu: Crystallographic and kinetic studies of human mitochondrial aceto... -

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Basic information

Entry
Database: PDB / ID: 2ibu
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 / fatty acid beta-oxidation / response to starvation / 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, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / 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
COENZYME A / Acetyl-CoA acetyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 12, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)169,50013
Polymers166,1964
Non-polymers3,3049
Water21,0961171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19200 Å2
ΔGint-110 kcal/mol
Surface area51380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.249, 106.569, 101.497
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU1AA176144
21GLUGLUGLUGLU1BB176144
31GLUGLUGLUGLU1CC176144
41GLUGLUGLUGLU1DD176144
12ASPASPILEILE3AA177 - 179145 - 147
22ASPASPILEILE3BB177 - 179145 - 147
32ASPASPILEILE3CC177 - 179145 - 147
42ASPASPILEILE3DD177 - 179145 - 147
13GLYGLYTHRTHR3AA183 - 185151 - 153
23GLYGLYTHRTHR3BB183 - 185151 - 153
33GLYGLYTHRTHR3CC183 - 185151 - 153
43GLYGLYTHRTHR3DD183 - 185151 - 153
14PHEPHEVALVAL3AA325 - 330293 - 298
24PHEPHEVALVAL3BB325 - 330293 - 298
34PHEPHEVALVAL3CC325 - 330293 - 298
44PHEPHEVALVAL3DD325 - 330293 - 298

NCS ensembles :
ID
1
2
3
4
DetailsThe asymmetric unit consists of one biological unit, the homotetramer

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Components

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


Mass: 41549.047 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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.57 %
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: X11 / Wavelength: 0.8115 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 6, 2004 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8115 Å / Relative weight: 1
ReflectionResolution: 1.9→19.46 Å / Num. all: 122801 / Num. obs: 122616 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 16
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.3 / Num. unique all: 17454 / Rsym value: 0.347 / % possible all: 100

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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: 1.9→19.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.85 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19772 6131 5 %RANDOM
Rwork0.16559 ---
obs0.16719 116484 100 %-
all-122615 --
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: 26.242 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.09 Å2
2--0.38 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11522 0 202 1171 12895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211936
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.99916194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0715.0511572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15825.9400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.932152083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5651536
X-RAY DIFFRACTIONr_chiral_restr0.0880.21924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028588
X-RAY DIFFRACTIONr_nbd_refined0.2020.26412
X-RAY DIFFRACTIONr_nbtor_refined0.2970.28414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.21250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.231
X-RAY DIFFRACTIONr_mcbond_it1.42838024
X-RAY DIFFRACTIONr_mcangle_it1.995412494
X-RAY DIFFRACTIONr_scbond_it1.55834424
X-RAY DIFFRACTIONr_scangle_it2.19743700
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A9tight positional0.130.05
12B9tight positional0.390.05
13C9tight positional0.130.05
14D9tight positional0.130.05
21A12tight positional0.020.05
22B12tight positional0.020.05
23C12tight positional0.020.05
24D12tight positional0.010.05
31A12tight positional0.020.05
32B12tight positional0.030.05
33C12tight positional0.020.05
34D12tight positional0.030.05
41A24tight positional0.020.05
42B24tight positional0.030.05
43C24tight positional0.030.05
44D24tight positional0.030.05
21A12loose positional0.065
22B12loose positional0.095
23C12loose positional0.125
24D12loose positional0.085
31A7loose positional0.075
32B7loose positional0.085
33C7loose positional0.085
34D7loose positional0.135
41A21loose positional0.065
42B21loose positional0.085
43C21loose positional0.065
44D21loose positional0.115
11A9tight thermal0.120.5
12B9tight thermal0.190.5
13C9tight thermal0.120.5
14D9tight thermal0.180.5
21A12tight thermal0.560.5
22B12tight thermal0.310.5
23C12tight thermal0.280.5
24D12tight thermal0.530.5
31A12tight thermal0.650.5
32B12tight thermal0.250.5
33C12tight thermal0.280.5
34D12tight thermal0.620.5
41A24tight thermal0.740.5
42B24tight thermal0.440.5
43C24tight thermal0.520.5
44D24tight thermal0.650.5
21A12loose thermal4.2510
22B12loose thermal3.1210
23C12loose thermal2.8310
24D12loose thermal4.1410
31A7loose thermal4.910
32B7loose thermal1.2610
33C7loose thermal2.2710
34D7loose thermal3.7810
41A21loose thermal5.410
42B21loose thermal2.4410
43C21loose thermal2.710
44D21loose thermal4.9210
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.246 885 -
Rwork0.196 16820 -
obs-16820 100 %

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