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- PDB-4dd5: Biosynthetic Thiolase (ThlA1) from Clostridium difficile -

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Basic information

Entry
Database: PDB / ID: 4dd5
TitleBiosynthetic Thiolase (ThlA1) from Clostridium difficile
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / thiolase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm
Similarity search - Function
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 ...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
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Biosynthetic Thiolase (ThlA1) from Clostridium difficile
Authors: Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,4351
Polymers41,4351
Non-polymers00
Water9,152508
1
A: Acetyl-CoA acetyltransferase

A: Acetyl-CoA acetyltransferase

A: Acetyl-CoA acetyltransferase

A: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)165,7394
Polymers165,7394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area13840 Å2
ΔGint-79 kcal/mol
Surface area47820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.850, 107.411, 151.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

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Components

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


Mass: 41434.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_10590, thlA, thlA1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q18AR0, acetyl-CoA C-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M NH4 Citrate, 0.1 M Bis-Tris, Propane, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. all: 131046 / Num. obs: 131046 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.4
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6295 / % possible all: 96.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dlv

1dlv


Resolution: 1.25→29.128 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.93 / SU ML: 0.018 / Isotropic thermal model: MIXED ISOTROPIC AND ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13508 6598 5 %RANDOM
Rwork0.11669 ---
obs0.11761 124443 99.21 %-
all-124443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2---0.91 Å20 Å2
3----0.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.25→29.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 0 508 3317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193074
X-RAY DIFFRACTIONr_bond_other_d0.0010.022035
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9794186
X-RAY DIFFRACTIONr_angle_other_deg1.02235042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59825.536112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9715554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4631516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02563
X-RAY DIFFRACTIONr_rigid_bond_restr4.00233074
X-RAY DIFFRACTIONr_sphericity_free19.708520
X-RAY DIFFRACTIONr_sphericity_bonded9.41853210
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 442 -
Rwork0.239 8034 -
obs--90.66 %

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