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

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Basic information

Entry
Database: PDB / ID: 4jat
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
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: 2.42 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 1.1May 21, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,6868
Polymers150,6604
Non-polymers1,0264
Water5,296294
1
A: Alpha-pyrone synthesis polyketide synthase-like Pks11
C: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8434
Polymers75,3302
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-16 kcal/mol
Surface area24190 Å2
MethodPISA
2
B: Alpha-pyrone synthesis polyketide synthase-like Pks11
D: Alpha-pyrone synthesis polyketide synthase-like Pks11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8434
Polymers75,3302
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-16 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.374, 48.871, 194.616
Angle α, β, γ (deg.)90.00, 97.95, 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: 37665.078 Da / Num. of mol.: 4 / Mutation: C138S
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.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M SODIUM ACETATE, 6% PEG 4K AND 10% ISOPROPANOL, pH 5.2, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.42→37.65 Å / Num. all: 51828 / Num. obs: 47290 / % possible obs: 96 % / Observed criterion σ(F): 13 / Observed criterion σ(I): 2.7

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Processing

Software
NameClassification
HKL-2000data collection
MLPHAREphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→37.65 Å
RfactorNum. reflection% reflection
Rfree0.27626 2541 5.1 %
Rwork0.19598 --
obs0.20013 47290 96.5 %
all-51828 -
Refinement stepCycle: LAST / Resolution: 2.42→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10568 0 72 294 10934

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