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- PDB-4wyr: Crystal structure of thiolase mutation (V77Q,N153Y,A286K) from Cl... -

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Basic information

Entry
Database: PDB / ID: 4wyr
TitleCrystal structure of thiolase mutation (V77Q,N153Y,A286K) from Clostridium acetobutylicum
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


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
DI(HYDROXYETHYL)ETHER / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKim, S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Lim, J.H. / Kim, K.J.
CitationJournal: Nat Commun / Year: 2015
Title: Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum
Authors: Kim, S. / Jang, Y.S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Hong Lim, J. / Cho, C. / Shin Ryu, Y. / Kuk Lee, S. / Lee, S.Y. / Kim, K.J.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Other
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7109
Polymers84,9952
Non-polymers7157
Water4,702261
1
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules

A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,42018
Polymers169,9914
Non-polymers1,43014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area18990 Å2
ΔGint-32 kcal/mol
Surface area50800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.434, 131.201, 54.120
Angle α, β, γ (deg.)90.000, 110.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42497.730 Da / Num. of mol.: 2 / Mutation: V77Q, N153Y, A286K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: thlA, thl, CA_C2873 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P45359, acetyl-CoA C-acetyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: PEG 3350, K-citrate, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34051 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 34.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 10.4 / Rejects: 0 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N45

4n45


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1531 / FOM work R set: 0.8551 / SU B: 6.052 / SU ML: 0.148 / SU R Cruickshank DPI: 0.3196 / SU Rfree: 0.2187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 1690 5 %RANDOM
Rwork0.1506 ---
obs0.1538 31912 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.34 Å2 / Biso mean: 33.147 Å2 / Biso min: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å2-0 Å2-0.34 Å2
2---1.94 Å2-0 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 0 47 261 6112
Biso mean--55.91 35.93 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195928
X-RAY DIFFRACTIONr_bond_other_d0.0020.025919
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9747977
X-RAY DIFFRACTIONr_angle_other_deg1.009313647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78425.495222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9051524
X-RAY DIFFRACTIONr_chiral_restr0.1020.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026708
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021204
X-RAY DIFFRACTIONr_mcbond_it2.3683.0093134
X-RAY DIFFRACTIONr_mcbond_other2.3673.0083133
X-RAY DIFFRACTIONr_mcangle_it3.5184.5033914
LS refinement shellResolution: 2.295→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 98 -
Rwork0.182 2183 -
all-2281 -
obs--90.02 %

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