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- PDB-4xl3: Crystal structure of reduced form of thiolase from Clostridium ac... -

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Basic information

Entry
Database: PDB / ID: 4xl3
TitleCrystal structure of reduced form of thiolase from Clostridium acetobutylicum
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, 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 ...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 speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,2448
Polymers84,6912
Non-polymers5536
Water14,160786
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-22 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.416, 54.290, 73.277
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, N-acetylornithine carbamoyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 786 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
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: 1.7→50 Å / Num. obs: 90712 / % possible obs: 97.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 43.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 11.3 / Rejects: 0 / % possible all: 91

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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: 4N44

4n44


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1979 / WRfactor Rwork: 0.1588 / FOM work R set: 0.9068 / SU B: 1.607 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0909 / SU Rfree: 0.0942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 4449 5 %RANDOM
Rwork0.1529 84226 --
obs0.1548 84226 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.19 Å2 / Biso mean: 21.856 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-0 Å2
2--0.65 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 36 786 6622
Biso mean--33.26 32.85 -
Num. residues----786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0196067
X-RAY DIFFRACTIONr_bond_other_d0.0010.026048
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.9738196
X-RAY DIFFRACTIONr_angle_other_deg0.944313951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67425.234235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.062151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9461531
X-RAY DIFFRACTIONr_chiral_restr0.1370.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026957
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021254
X-RAY DIFFRACTIONr_mcbond_it2.0831.843204
X-RAY DIFFRACTIONr_mcbond_other2.0831.8393203
X-RAY DIFFRACTIONr_mcangle_it2.9442.7514022
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 279 -
Rwork0.177 5687 -
all-5966 -
obs--90.18 %

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