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- PDB-1mnq: Thioesterase Domain of Picromycin Polyketide Synthase (PICS TE), ... -

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Basic information

Entry
Database: PDB / ID: 1mnq
TitleThioesterase Domain of Picromycin Polyketide Synthase (PICS TE), pH 8.4
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 / 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 / PKS_PP_betabranch / Thioesterase / Thioesterase domain / 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 / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / 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
Narbonolide/10-deoxymethynolide synthase PikA4, module 6
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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-16 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.016, 106.224, 114.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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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 / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.83 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 30% PEG 4000, 100 mM Tris, 2 mM DTT, 100 mM lithium sulfate, pH 8.4, 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 %PEG40001reservoir
2100 mMTris1reservoirpH8.4
32 mMdithiothreitol1reservoir
4100 mM1reservoirLiSO4
510 mg/mlprotein1drop
610 mMHEPES1droppH7.5
72 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2001 / Details: double crystals
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 35346 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % possible obs: 97.4 % / Num. measured all: 418911
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMAC5refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24834 1858 5 %RANDOM
Rwork0.21966 ---
all0.221 35344 --
obs0.22115 35344 99.92 %-
Displacement parametersBiso mean: 18.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---0.95 Å20 Å2
3---0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 0 340 4523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0170.0214297
X-RAY DIFFRACTIONp_angle_deg1.7411.9625857
X-RAY DIFFRACTIONp_angle_d1.7411.9625857
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214297
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9625857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8813548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.81215691
X-RAY DIFFRACTIONr_chiral_restr0.1280.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023434
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3220.32400
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2890.5444
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.336
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8451.52750
X-RAY DIFFRACTIONr_mcangle_it1.52424353
X-RAY DIFFRACTIONr_scbond_it2.82931547
X-RAY DIFFRACTIONr_scangle_it4.4554.51504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 125
Rwork0.255 2570
Refinement
*PLUS
Highest resolution: 2.2 Å / Num. reflection obs: 30344 / σ(F): 0 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.74

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