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- PDB-1m3k: biosynthetic thiolase, inactive C89A mutant -

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Basic information

Entry
Database: PDB / ID: 1m3k
Titlebiosynthetic thiolase, inactive C89A mutant
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase fold
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm
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
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKursula, P. / Ojala, J. / Lambeir, A.-M. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2002
Title: The catalytic cycle of biosynthetic thiolase: A conformational journey of an acetyl group through four binding modes and two oxyanion holes
Authors: Kursula, P. / Ojala, J. / Lambeir, A.-M. / Wierenga, R.K.
History
DepositionJun 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: 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)162,60510
Polymers162,0374
Non-polymers5686
Water20,8791159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-104 kcal/mol
Surface area50340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.370, 79.199, 148.863
Angle α, β, γ (deg.)90.00, 92.32, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Acetyl-CoA acetyltransferase / E.C.2.3.1.9 / Acetoacetyl-CoA thiolase / biosynthetic thiolase


Mass: 40509.145 Da / Num. of mol.: 4 / Mutation: C89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoogloea ramigera (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1159 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: lithium sulphate, ammonium sulphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP at 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium citrate1reservoirpH5.0
21.0 M1reservoirLi2SO4
30.9 Mammonium sulfate1reservoir
41 mMEDTA1reservoir
51 mMdithiothreitol1reservoir
61 mM1reservoirNaN3
72 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.915 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 193811 / Num. obs: 193811 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.079 / Net I/σ(I): 10.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 19129 / Rsym value: 0.329 / % possible all: 56.7
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 56.7 % / Rmerge(I) obs: 0.329

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLU

1dlu


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, TLS parameterisation / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24296 8981 4.6 %RANDOM
Rwork0.19924 ---
all0.20126 193695 --
obs0.20126 193695 90.07 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.72 Å2
2---1.36 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11328 0 32 1159 12519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02111530
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210722
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.95315578
X-RAY DIFFRACTIONr_angle_other_deg0.931324862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251564
X-RAY DIFFRACTIONr_chiral_restr0.1130.21756
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213208
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022208
X-RAY DIFFRACTIONr_nbd_refined0.2230.22811
X-RAY DIFFRACTIONr_nbd_other0.250.213153
X-RAY DIFFRACTIONr_nbtor_other0.0870.26774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2879
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.239
X-RAY DIFFRACTIONr_mcbond_it2.40947704
X-RAY DIFFRACTIONr_mcangle_it3.161512144
X-RAY DIFFRACTIONr_scbond_it3.44853826
X-RAY DIFFRACTIONr_scangle_it4.76963434
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.266 395
Rwork0.231 7503
obs-7898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7677-0.4226-0.01780.8610.01710.1633-0.0296-0.0534-0.00040.06590.0311-0.006-0.00050.0008-0.00150.0225-0.00840.03830.12500.067121.108-0.0726.689
20.5232-0.09430.0550.82470.14710.70290.0503-0.0088-0.0150.181-0.05790.08030.0177-0.07830.00760.51830.0185-0.08570.3045-0.00450.232623.5760.42161.932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3921 - 392
2X-RAY DIFFRACTION1BB1 - 3921 - 392
3X-RAY DIFFRACTION2CC1 - 3921 - 392
4X-RAY DIFFRACTION2DD1 - 3921 - 392
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 184714 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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