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- PDB-1mn6: Thioesterase Domain from Picromycin Polyketide Synthase, pH 7.6 -

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Basic information

Entry
Database: PDB / ID: 1mn6
TitleThioesterase Domain from Picromycin Polyketide Synthase, pH 7.6
Componentspolyketide synthase IV
KeywordsTRANSFERASE / thioesterase / polyketide synthase / open substrate channel / alpha-beta hydrolase
Function / homology
Function and homology information


10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pikromycin polyketide synthase component PikAIV
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTsai, S.-C. / Lu, H. / Cane, D.E. / Khosla, C. / Stroud, R.M.
CitationJournal: Biochemistry / Year: 2002
Title: Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases
Authors: Tsai, S.-C. / Lu, H. / Cane, D.E. / Khosla, C. / Stroud, R.M.
History
DepositionSep 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: polyketide synthase IV
B: polyketide synthase IV


Theoretical massNumber of molelcules
Total (without water)62,9702
Polymers62,9702
Non-polymers00
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-15 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.120, 58.330, 90.930
Angle α, β, γ (deg.)90.00, 96.16, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein polyketide synthase IV / Picromycin Polyketide Synthase / PikAIV / type I polyketide synthase PikAIV


Mass: 31485.240 Da / Num. of mol.: 2 / Fragment: Thioesterase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: picAIV / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZGI2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.38 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 30% PEG 8000, 100 mM HEPES, 2 mM DTT, 100 mM magnesium chloride, pH 7.6, VAPOR DIFFUSION, SITTING DROP at 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %PEG80001reservoir
2100 mMHEPES1reservoirpH7.6
32 mMdithiothreitol1reservoir
4100 mM1reservoirMgCl2
510 mg/mlprotein1drop
610 mMHEPES1droppH7.5
72 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 31231 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.3
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 203580
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
Blu-Icedata collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEZ

1kez


Resolution: 2.2→29.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 208419.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1498 5 %RANDOM
Rwork0.192 ---
all0.192 31078 --
obs0.192 30136 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4463 Å2 / ksol: 0.360028 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å24.1 Å2
2--0.36 Å20 Å2
3----0.66 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 0 446 4637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 254 5.3 %
Rwork0.211 4565 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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