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- PDB-4n44: Crystal structure of oxidized form of thiolase from Clostridium a... -

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Basic information

Entry
Database: PDB / ID: 4n44
TitleCrystal structure of oxidized form of thiolase from Clostridium acetobutylicum
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / alpha/beta/alpha/beta/alpha domain / Acetyl-coA acetyltransferase
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / :
Function and homology information
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsKim, S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Lim, J.H. / Kim, K.J.
CitationJournal: to be published
Title: Structural insight into redox-switch regulatory mechanism of thiolase from the n-butanol synthesizing bacterium, Clostridium acetobutylicum
Authors: Kim, S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Lim, J.H. / Son, H.C. / Ryu, Y.S. / Lee, S.K. / Kim, K.J.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
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 / 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)85,1438
Polymers84,7232
Non-polymers4206
Water7,873437
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)170,28716
Polymers169,4464
Non-polymers84112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17870 Å2
ΔGint-84 kcal/mol
Surface area54560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.227, 53.987, 72.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 42361.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: EA 2018 / Gene: CEA_G2880 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: F0K5D8, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 437 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 49.25 % / Mosaicity: 0.493 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG3350, K-citrate, NaCl, pH 4.2, vapor diffusion, hanging drop, temperature 295K

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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
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionRedundancy: 5.3 % / Number: 410057 / Rmerge(I) obs: 0.07 / Χ2: 1.76 / D res high: 1.77 Å / D res low: 50 Å / Num. obs: 77934 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
1.771.8387.910.2990.6024.1
1.831.9198.310.2470.6894.5
1.911.9999.210.2030.8425
1.992.199.410.151.0845.3
2.12.2399.510.1271.3085.4
2.232.499.410.1061.65.5
2.42.6499.410.0931.9325.6
2.643.0399.310.0762.2875.7
3.033.8199.610.0612.9575.9
3.81509910.0513.1875.5
ReflectionResolution: 1.77→50 Å / Num. all: 79061 / Num. obs: 77934 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.063 / Net I/σ(I): 33.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.77-1.834.10.2992.868690.27687.9
1.83-1.914.50.2474.176830.22498.3
1.91-1.9950.2036.577890.18399.2
1.99-2.15.30.1510.578270.13799.4
2.1-2.235.40.12714.678190.12199.5
2.23-2.45.50.10620.578400.10499.4
2.4-2.645.60.09326.278720.09599.4
2.64-3.035.70.07635.879370.07999.3
3.03-3.815.90.06151.679880.06599.6
3.81-505.50.05157.583100.05999

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLV

1dlv


Resolution: 1.77→43.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.299 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 3911 5 %RANDOM
Rwork0.1681 ---
all0.1702 77903 --
obs0.1702 73992 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.27 Å2 / Biso mean: 30.7619 Å2 / Biso min: 13.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å20 Å2
2--2.68 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.77→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 28 437 6249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195890
X-RAY DIFFRACTIONr_bond_other_d0.0010.025872
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9727942
X-RAY DIFFRACTIONr_angle_other_deg0.9163.00113524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84225.545220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.011524
X-RAY DIFFRACTIONr_chiral_restr0.1310.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021196
X-RAY DIFFRACTIONr_mcbond_it2.8752.963138
X-RAY DIFFRACTIONr_mcbond_other2.862.9593133
X-RAY DIFFRACTIONr_mcangle_it4.1864.4263914
LS refinement shellResolution: 1.77→1.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 233 -
Rwork0.233 4944 -
all-5177 -
obs--89.29 %

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