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- PDB-3goa: Crystal structure of the Salmonella typhimurium FadA 3-ketoacyl-C... -

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Basic information

Entry
Database: PDB / ID: 3goa
TitleCrystal structure of the Salmonella typhimurium FadA 3-ketoacyl-CoA thiolase
Components3-ketoacyl-CoA thiolase
KeywordsTRANSFERASE / metabolism / fatty acid / phospholipid / IDP01071 / Acyltransferase / Cytoplasm / Fatty acid metabolism / Lipid degradation / Lipid metabolism / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / fatty acid beta-oxidation / cytoplasm
Similarity search - Function
Acetyl-CoA C-acyltransferase FadA / : / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain ...Acetyl-CoA C-acyltransferase FadA / : / Thiolase, active site / Thiolases active site. / 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
3-ketoacyl-CoA thiolase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsAnderson, S.M. / Skarina, T. / Onopriyenko, O. / Wawrzak, Z. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

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Assembly

Deposited unit
A: 3-ketoacyl-CoA thiolase
B: 3-ketoacyl-CoA thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1507
Polymers83,9762
Non-polymers1745
Water17,583976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-49 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.0, 64.5, 74.4
Angle α, β, γ (deg.)90.0, 104.5, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-ketoacyl-CoA thiolase / Fatty acid oxidation complex subunit beta / Beta-ketothiolase / Acetyl-CoA acyltransferase


Mass: 41988.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: fadA, STM3982, STMD1.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2H7, acetyl-CoA C-acyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 976 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG3350, 50mM calcium chloride, 100mM tris, 5mM Acetyl-CoA, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 74330 / Num. obs: 73958 / % possible obs: 99.5 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.126 / Χ2: 1.031 / Net I/σ(I): 13.14
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.4 / Num. unique all: 7166 / Χ2: 0.931 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
BLU-MAXdata collection
SHARPphasing
RefinementResolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.147 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.897 / SU B: 1.841 / SU ML: 0.062 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.097 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3730 5 %RANDOM
Rwork0.142 ---
all0.145 74330 --
obs0.145 73939 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.61 Å2 / Biso mean: 16.997 Å2 / Biso min: 3.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.02 Å2
2---0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5742 0 5 1001 6748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225842
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9677920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24123.219233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.826151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8481551
X-RAY DIFFRACTIONr_chiral_restr0.0980.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214382
X-RAY DIFFRACTIONr_mcbond_it1.731.53815
X-RAY DIFFRACTIONr_mcangle_it2.68226102
X-RAY DIFFRACTIONr_scbond_it4.46632027
X-RAY DIFFRACTIONr_scangle_it6.7694.51800
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 237 -
Rwork0.218 4812 -
all-5049 -
obs-4740 92.56 %

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