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- PDB-1ted: Crystal structure of a type III polyketide synthase PKS18 from My... -

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Basic information

Entry
Database: PDB / ID: 1ted
TitleCrystal structure of a type III polyketide synthase PKS18 from Mycobacterium tuberculosis
Componentspks18
KeywordsTRANSFERASE / thiolase fold / substrate binding tunnel
Function / homology
Function and homology information


chalcone biosynthetic process / polyketide 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 / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / Alpha-pyrone synthesis polyketide synthase-like Pks18 / Alpha-pyrone synthesis polyketide synthase-like Pks18
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSankaranarayanan, R. / Shanmugam, V.M. / Rukmini, R.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: A novel tunnel in mycobacterial type III polyketide synthase reveals the structural basis for generating diverse metabolites
Authors: Sankaranarayanan, R. / Saxena, P. / Marathe, U.B. / Gokhale, R.S. / Shanmugam, V.M. / Rukmini, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray crystallographic investigations of an unusual type III polyketide synthase PKS18 from Mycobacterium tuberculosis
Authors: Rukmini, R. / Shanmugam, V.M. / Saxena, P. / Gokhale, R.S. / Sankaranarayanan, R.
History
DepositionMay 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: pks18
B: pks18
C: pks18
D: pks18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,2078
Polymers168,2934
Non-polymers9134
Water19,9251106
1
A: pks18
B: pks18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6034
Polymers84,1472
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-7 kcal/mol
Surface area26530 Å2
MethodPISA
2
C: pks18
D: pks18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6034
Polymers84,1472
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-5 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.914, 80.654, 99.612
Angle α, β, γ (deg.)108.23, 92.97, 103.69
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a homodimer. The file contains two of them, AB and CD.

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Components

#1: Protein
pks18 / polyketide synthase


Mass: 42073.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: pks18 / Plasmid: pET21C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7D8I1, UniProt: P9WPF1*PLUS, chalcone synthase
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 2.5 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 8000, HEPES, ethylene glycol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. all: 80874 / Num. obs: 76912 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.74 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.25→2.36 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2 / Num. unique all: 7360 / % possible all: 91.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGZ

1cgz


Resolution: 2.25→24.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1677848.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3858 5 %RANDOM
Rwork0.205 ---
obs0.205 76912 95 %-
all-76912 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9511 Å2 / ksol: 0.328374 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.77 Å20.5 Å2-2.32 Å2
2---2.35 Å2-0.4 Å2
3----3.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-10 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10856 0 64 1106 12026
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 2.25→2.33 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 385 5.2 %
Rwork0.28 6994 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMCNS_ION.TOP
X-RAY DIFFRACTION4MYR.PARAM

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