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

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Basic information

Entry
Database: PDB / ID: 4jao
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-methylheptadecan-1-ol / 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 / MAD / Resolution: 2.05 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 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
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)151,7788
Polymers150,7254
Non-polymers1,0544
Water6,936385
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)75,8894
Polymers75,3622
Non-polymers5272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-17 kcal/mol
Surface area23090 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)75,8894
Polymers75,3622
Non-polymers5272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-16 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.123, 48.426, 189.694
Angle α, β, γ (deg.)90.00, 97.25, 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-JAO / (2S)-2-methylheptadecan-1-ol


Mass: 270.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M sodium acetate trihydrate, 5.6% PEG 4000, 10% isopropanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979, 0.97179
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.971791
ReflectionResolution: 2.05→47.04 Å / Num. obs: 63039 / % possible obs: 92 % / Observed criterion σ(F): 11.66 / Observed criterion σ(I): 6.39

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→47.04 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 34.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 3158 5.01 %
Rwork0.211 --
obs0.214 63025 77 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.05 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4375 Å2-0 Å2-5.7154 Å2
2---2.7344 Å2-0 Å2
3----1.7031 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10568 0 74 385 11027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910852
X-RAY DIFFRACTIONf_angle_d1.32714766
X-RAY DIFFRACTIONf_dihedral_angle_d18.8313994
X-RAY DIFFRACTIONf_chiral_restr0.0861726
X-RAY DIFFRACTIONf_plane_restr0.0051924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07590.2701220.2925426X-RAY DIFFRACTION13
2.0759-2.10840.4115530.29181128X-RAY DIFFRACTION33
2.1084-2.14290.3443530.30481219X-RAY DIFFRACTION37
2.1429-2.17990.3601650.291346X-RAY DIFFRACTION40
2.1799-2.21950.3441870.28771521X-RAY DIFFRACTION45
2.2195-2.26220.3302970.27551835X-RAY DIFFRACTION55
2.2622-2.30840.3561910.25982044X-RAY DIFFRACTION60
2.3084-2.35860.33451300.28372140X-RAY DIFFRACTION65
2.3586-2.41340.32491430.26832455X-RAY DIFFRACTION73
2.4134-2.47380.3891410.27172660X-RAY DIFFRACTION80
2.4738-2.54070.35251430.27052961X-RAY DIFFRACTION86
2.5407-2.61540.32261570.26653115X-RAY DIFFRACTION94
2.6154-2.69980.29481480.25953303X-RAY DIFFRACTION97
2.6998-2.79630.32131510.25583292X-RAY DIFFRACTION97
2.7963-2.90830.31411660.24873263X-RAY DIFFRACTION97
2.9083-3.04060.29891980.24313299X-RAY DIFFRACTION97
3.0406-3.20090.29511820.22773343X-RAY DIFFRACTION99
3.2009-3.40140.31831860.21213336X-RAY DIFFRACTION99
3.4014-3.66390.26111840.20023382X-RAY DIFFRACTION100
3.6639-4.03240.2631850.17663412X-RAY DIFFRACTION100
4.0324-4.61550.21591800.15283399X-RAY DIFFRACTION100
4.6155-5.81330.23811930.18643444X-RAY DIFFRACTION100
5.8133-47.040.21192030.18313544X-RAY DIFFRACTION100

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