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- PDB-4xl4: Crystal structure of thiolase from Clostridium acetobutylicum in ... -

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Basic information

Entry
Database: PDB / ID: 4xl4
TitleCrystal structure of thiolase from Clostridium acetobutylicum in complex with CoA
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


N-acetylornithine carbamoyltransferase activity / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity
Similarity search - Function
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 ...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 C-acetyltransferase / :
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJan 13, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 7, 2015ID: 4N46
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Derived calculations
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)86,87111
Polymers84,6912
Non-polymers2,1809
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-22 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.307, 54.171, 73.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is the same as asym.

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Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 42345.496 Da / Num. of mol.: 2 / Mutation: C378S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (strain EA 2018) (bacteria)
Strain: EA 2018 / Gene: CEA_G2880 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: F0K5D8, UniProt: A0A0R4I970*PLUS, acetyl-CoA C-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
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: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 23, 2014
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 65291 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 33.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 5.6 / Rejects: 0 / % possible all: 99.9

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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: 1.9→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1776 / WRfactor Rwork: 0.1383 / FOM work R set: 0.9105 / SU B: 2.525 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1177 / SU Rfree: 0.1155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 3291 5.1 %RANDOM
Rwork0.142 61614 --
obs0.1441 61614 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.3 Å2 / Biso mean: 24.167 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0 Å2
2--0.5 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 138 636 6558
Biso mean--37.9 33.59 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196040
X-RAY DIFFRACTIONr_bond_other_d0.0010.025970
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.9928160
X-RAY DIFFRACTIONr_angle_other_deg0.899313767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48225.625224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.872151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3321524
X-RAY DIFFRACTIONr_chiral_restr0.1210.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021228
X-RAY DIFFRACTIONr_mcbond_it1.942.0433154
X-RAY DIFFRACTIONr_mcbond_other1.942.0423153
X-RAY DIFFRACTIONr_mcangle_it2.6973.0533946
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 230 -
Rwork0.172 4384 -
all-4614 -
obs--97.47 %

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