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- PDB-1jmk: Structural Basis for the Cyclization of the Lipopeptide Antibioti... -

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Basic information

Entry
Database: PDB / ID: 1jmk
TitleStructural Basis for the Cyclization of the Lipopeptide Antibiotic Surfactin by the Thioesterase Domain SrfTE
ComponentsSurfactin Synthetase
KeywordsHYDROLASE / Thioesterase / Non-ribosomal Peptide Synthesis / Alpha-beta Hydrolase / Cyclic Peptide
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / sporulation resulting in formation of a cellular spore / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Helix hairpin bin / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily ...Helix hairpin bin / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / 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 / Helix Hairpins / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Surfactin synthase subunit 3
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.71 Å
AuthorsBruner, S.D. / Weber, T. / Kohli, R.M. / Schwarzer, D. / Marahiel, M.A. / Walsh, C.T. / Stubbs, M.T.
CitationJournal: Structure / Year: 2002
Title: Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE.
Authors: Bruner, S.D. / Weber, T. / Kohli, R.M. / Schwarzer, D. / Marahiel, M.A. / Walsh, C.T. / Stubbs, M.T.
History
DepositionJul 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
C: Surfactin Synthetase
O: Surfactin Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5784
Polymers51,3862
Non-polymers1922
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.01, 76.37, 119.71
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Surfactin Synthetase / SrfTE


Mass: 25692.805 Da / Num. of mol.: 2 / Fragment: Thioesterase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SrfA-C / Plasmid: pQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08787
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8M Ammonium Sulfate, 0.1M HEPES 7.5, 2% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.5
21.8 Mammonium sulfate1reservoir
32 %MPD1reservoir
410 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONMPG/DESY, HAMBURG BW610.95, 0.9799, 0.9807
SYNCHROTRONCHESS A120.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 25, 2001
ADSC QUANTUM 42CCDFeb 27, 2001
RadiationMonochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97991
30.98071
40.9791
ReflectionResolution: 1.71→25 Å / Num. all: 63148 / Num. obs: 62391 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.71→1.77 Å / % possible all: 92.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 663308 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 92.5 % / Num. unique obs: 5717 / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.71→25 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 2838 random
Rwork0.23 --
all-63753 -
obs-62391 -
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.71→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 10 238 3779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 1.71→1.82 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.322 896 -
Rwork0.308 --
obs-8556 81.5 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 10 % / Rfactor obs: 0.222 / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.269
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / Rfactor Rwork: 0.308 / Rfactor obs: 0.308

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