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- PDB-1kez: Crystal Structure of the Macrocycle-forming Thioesterase Domain o... -

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Basic information

Entry
Database: PDB / ID: 1kez
TitleCrystal Structure of the Macrocycle-forming Thioesterase Domain of Erythromycin Polyketide Synthase (DEBS TE)
ComponentsERYTHRONOLIDE SYNTHASE
KeywordsTRANSFERASE / polyketide synthase / 6-deoxyerythronolide synthase / modular polyketide synthase / thioesterase / 6-dEB / TE / DEBS / alpha / beta-hydrolase / macrocycle
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase, docking domain superfmaily / 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 ...Polyketide synthase, docking domain superfmaily / 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 / Polyketide synthase, ketoreductase domain / KR domain / 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. / PKS_KR / 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 / Phosphopantetheine attachment site. / 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 / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsTsai, S.-C. / Miercke, L.J.W. / Krucinski, J. / Gokhale, R. / Chen, J.C.-H. / Foster, P.G. / Cane, D.E. / Khosla, C. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel.
Authors: Tsai, S.C. / Miercke, L.J. / Krucinski, J. / Gokhale, R. / Chen, J.C. / Foster, P.G. / Cane, D.E. / Khosla, C. / Stroud, R.M.
History
DepositionNov 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ERYTHRONOLIDE SYNTHASE
B: ERYTHRONOLIDE SYNTHASE
C: ERYTHRONOLIDE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)96,3383
Polymers96,3383
Non-polymers00
Water7,080393
1
A: ERYTHRONOLIDE SYNTHASE
B: ERYTHRONOLIDE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)64,2262
Polymers64,2262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16 kcal/mol
Surface area29580 Å2
MethodPISA
2
C: ERYTHRONOLIDE SYNTHASE

C: ERYTHRONOLIDE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)64,2262
Polymers64,2262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)130.500, 130.500, 208.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsDEBS TE is a homodimer: the deposited monomers A-B is related by NCS 2-fold, while monomers C-C' is related by crystallographic 2-fold

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Components

#1: Protein ERYTHRONOLIDE SYNTHASE / 6-DEOXYERYTHRONOLIDE B SYNTHASE III


Mass: 32112.768 Da / Num. of mol.: 3
Fragment: terminal thioesterase domain, module 6 (residues 2893-3172)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Plasmid: pET21c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q03133, 6-deoxyerythronolide-B synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2

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Sample preparation

CrystalDensity Matthews: 5.32 Å3/Da / Density % sol: 76.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG400, 0.1 M MgCl2, HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %PEG4001reservoir
2100 mMHEPES1reservoirpH7.5
32 mMdithiothreitol1reservoir
4100 mM1reservoirMgCl2
510 mg/mlprotein1drop
620 mMHEPES1droppH7.5
72 mMdithiothreitol1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211
SYNCHROTRONSSRL BL7-121.08
SYNCHROTRONSSRL BL9-130.98
SYNCHROTRONSSRL BL9-240.96-1.2
Detector
TypeIDDetectorDate
MARRESEARCH1AREA DETECTORDec 21, 1999
ADSC QUANTUM 42CCDMay 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.081
30.981
40.961
51.21
ReflectionResolution: 2.8→30 Å / Num. all: 51328 / Num. obs: 50859 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.031 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 50859 / Rsym value: 0.617 / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 190617 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
% possible obs: 93.1 % / Rmerge(I) obs: 0.617

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Processing

Software
NameClassification
CNSrefinement
XTALVIEWrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: CNS library
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2542 -random
Rwork0.254 ---
all0.256 50859 --
obs0.256 45998 99.1 %-
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.85 Å21.5 Å20 Å2
2---4.85 Å20 Å2
3---9.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.67 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6033 0 0 393 6426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg3
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d2.33
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.251 2542 -
Rwork0.241 --
obs-50859 99.1 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 1 / Rfactor obs: 0.241 / Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 71.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.33
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.241

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