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- PDB-4xl2: Crystal structure of oxidized form of thiolase from Clostridium a... -

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Basic information

Entry
Database: PDB / ID: 4xl2
TitleCrystal structure of oxidized form of thiolase 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, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / 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 / Thiolase, C-terminal / Thiolase, C-terminal domain / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 17, 2018Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / refine ...pdbx_struct_oper_list / refine / refine_ls_restr / refine_ls_shell
Item: _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_refine_id ..._pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_refine_id / _refine_ls_restr.pdbx_refine_id / _refine_ls_shell.pdbx_refine_id
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)85,87414
Polymers84,7232
Non-polymers1,15112
Water8,791488
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)171,74928
Polymers169,4464
Non-polymers2,30224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20590 Å2
ΔGint-38 kcal/mol
Surface area53170 Å2
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-7 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.227, 53.987, 72.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Acetoacetyl-CoA thiolase


Mass: 42361.559 Da / Num. of mol.: 2
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
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 210 / Detector: CCD / Date: Oct 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 79061 / % possible obs: 98.1 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.7
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.8 / % possible all: 87.9

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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: 1DLV

1dlv


Resolution: 1.77→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.564 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19102 3911 5 %RANDOM
Rwork0.15479 ---
obs0.15662 73992 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.174 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0 Å20 Å2
2--3.2 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 0 76 488 6238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195889
X-RAY DIFFRACTIONr_bond_other_d0.0010.025901
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.9767921
X-RAY DIFFRACTIONr_angle_other_deg0.893313602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59425.495222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.176151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3941526
X-RAY DIFFRACTIONr_chiral_restr0.1260.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021196
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7192.8393105
X-RAY DIFFRACTIONr_mcbond_other2.7142.8373102
X-RAY DIFFRACTIONr_mcangle_it3.8164.2343884
X-RAY DIFFRACTIONr_mcangle_other3.8154.2363885
X-RAY DIFFRACTIONr_scbond_it3.9313.3952784
X-RAY DIFFRACTIONr_scbond_other3.9193.3952784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.914.8384038
X-RAY DIFFRACTIONr_long_range_B_refined7.69724.126968
X-RAY DIFFRACTIONr_long_range_B_other7.57723.7486756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.772→1.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 234 -
Rwork0.257 4975 -
obs--89.9 %

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