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- PDB-4jap: Crystal Structure of Mycobacterium tuberculosis PKS11 Reveals Int... -

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Basic information

Entry
Database: PDB / ID: 4jap
TitleCrystal Structure of Mycobacterium tuberculosis PKS11 Reveals Intermediates in the Synthesis of Methyl-branched Alkylpyrones
ComponentsAlpha-pyrone synthesis polyketide synthase-like Pks11
KeywordsTRANSFERASE / lipid biosynthesis / Structural Genomics / Enzyme Function Initiative / ketosynthase enzyme / Alkylpyrone synthesis / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


polyketide synthase complex / chalcone biosynthetic process / polyketide biosynthetic process / DIM/DIP cell wall layer assembly / lipid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-methyl-3-oxooctadecanoic acid / COENZYME A / PALMITIC ACID / Methyl-branched alkylpyrone synthesis polyketide synthase-like Pks11 / Methyl-branched alkylpyrone synthesis polyketide synthase-like Pks11
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.833 Å
AuthorsGokulan, K. / Sacchettini, J.C. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal structure of Mycobacterium tuberculosis polyketide synthase 11 (PKS11) reveals intermediates in the synthesis of methyl-branched alkylpyrones.
Authors: Gokulan, K. / O'Leary, S.E. / Russell, W.K. / Russell, D.H. / Lalgondar, M. / Begley, T.P. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Alpha-pyrone synthesis polyketide synthase-like Pks11
C: Alpha-pyrone synthesis polyketide synthase-like Pks11
B: Alpha-pyrone synthesis polyketide synthase-like Pks11
A: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,39710
Polymers150,7254
Non-polymers2,6736
Water3,333185
1
D: Alpha-pyrone synthesis polyketide synthase-like Pks11
C: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6435
Polymers75,3622
Non-polymers1,2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-21 kcal/mol
Surface area24680 Å2
MethodPISA
2
B: Alpha-pyrone synthesis polyketide synthase-like Pks11
A: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7555
Polymers75,3622
Non-polymers1,3933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-27 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.011, 48.627, 193.656
Angle α, β, γ (deg.)90.00, 97.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-pyrone synthesis polyketide synthase-like Pks11 / Alpha-pyrone synthesis polyketide synthase type III Pks11 / Chalcone synthase-like protein / CHS-like


Mass: 37681.145 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: pks11, Rv1665, MT1705 / Production host: mycobacterium smegmatis (bacteria)
References: UniProt: O06587, UniProt: P9WPF3*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-14U / (2S)-2-methyl-3-oxooctadecanoic acid


Mass: 312.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium iodide, 20% w/v Polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 90986 / Observed criterion σ(F): 6.34 / Observed criterion σ(I): 0.22

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.833→44.803 Å / SU ML: 0.7 / σ(F): 1.33 / Phase error: 46.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.289 4291 5.01 %5%
Rwork0.2341 ---
obs0.2368 90962 77.37 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.212 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5629 Å2-0 Å2-5.7934 Å2
2---1.5784 Å2-0 Å2
3---0.0154 Å2
Refinement stepCycle: LAST / Resolution: 1.833→44.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10582 0 174 185 10941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110970
X-RAY DIFFRACTIONf_angle_d1.35414936
X-RAY DIFFRACTIONf_dihedral_angle_d17.3374026
X-RAY DIFFRACTIONf_chiral_restr0.0891742
X-RAY DIFFRACTIONf_plane_restr0.0051932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.833-1.85370.983210.90662X-RAY DIFFRACTION1
1.8537-1.87550.6447410.6374929X-RAY DIFFRACTION25
1.8755-1.89830.5361320.5747539X-RAY DIFFRACTION29
1.8983-1.92240.5038650.48071075X-RAY DIFFRACTION34
1.9224-1.94770.4693660.44881217X-RAY DIFFRACTION33
1.9477-1.97440.4686930.45871688X-RAY DIFFRACTION46
1.9744-2.00260.43731020.44641894X-RAY DIFFRACTION52
2.0026-2.03250.42041220.4252291X-RAY DIFFRACTION62
2.0325-2.06420.44221330.43262448X-RAY DIFFRACTION67
2.0642-2.09810.3611320.41232742X-RAY DIFFRACTION74
2.0981-2.13420.40831400.4072908X-RAY DIFFRACTION78
2.1342-2.1730.42551790.40053021X-RAY DIFFRACTION82
2.173-2.21480.42171580.38753212X-RAY DIFFRACTION87
2.2148-2.260.38121700.38493326X-RAY DIFFRACTION90
2.26-2.30920.4141700.35783487X-RAY DIFFRACTION93
2.3092-2.36290.36991990.34563546X-RAY DIFFRACTION97
2.3629-2.4220.40022020.32943693X-RAY DIFFRACTION98
2.422-2.48750.39822360.32313623X-RAY DIFFRACTION99
2.4875-2.56060.36761990.31773704X-RAY DIFFRACTION99
2.5606-2.64330.3891890.30193613X-RAY DIFFRACTION99
2.6433-2.73780.34391810.28413700X-RAY DIFFRACTION99
2.7378-2.84730.36992170.27073690X-RAY DIFFRACTION99
2.8473-2.97690.32562020.2643681X-RAY DIFFRACTION99
2.9769-3.13380.27951730.25023735X-RAY DIFFRACTION99
3.1338-3.33010.34161690.23113735X-RAY DIFFRACTION99
3.3301-3.58710.25352060.21633718X-RAY DIFFRACTION99
3.5871-3.94790.25791850.19843752X-RAY DIFFRACTION99
3.9479-4.51870.23411900.16493768X-RAY DIFFRACTION99
4.5187-5.69130.22112010.17463763X-RAY DIFFRACTION99
5.6913-44.8030.21772040.16643905X-RAY DIFFRACTION99

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