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- PDB-5t3e: Crystal structure of a nonribosomal peptide synthetase heterocycl... -

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Basic information

Entry
Database: PDB / ID: 5t3e
TitleCrystal structure of a nonribosomal peptide synthetase heterocyclization domain.
ComponentsBacillamide synthetase heterocyclization domain
KeywordsLIGASE / nonribosomal peptide synthetase / heterocyclization domain / natural products / thiazoline
Function / homology
Function and homology information


phosphopantetheine binding / catalytic activity
Similarity search - Function
Nonribosomal peptide synthetase, condensation domain / AMP-binding / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Nonribosomal peptide synthetase, condensation domain / AMP-binding / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsBloudoff, K. / Schmeing, T.M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural and mutational analysis of the nonribosomal peptide synthetase heterocyclization domain provides insight into catalysis.
Authors: Bloudoff, K. / Fage, C.D. / Marahiel, M.A. / Schmeing, T.M.
History
DepositionAug 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: 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: Bacillamide synthetase heterocyclization domain
B: Bacillamide synthetase heterocyclization domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7444
Polymers103,5522
Non-polymers1922
Water3,909217
1
A: Bacillamide synthetase heterocyclization domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8722
Polymers51,7761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bacillamide synthetase heterocyclization domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8722
Polymers51,7761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-27 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.693, 124.937, 68.925
Angle α, β, γ (deg.)90.00, 95.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bacillamide synthetase heterocyclization domain


Mass: 51775.801 Da / Num. of mol.: 2 / Fragment: unp residues 844-1287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: ADL26_17380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N0Y601
#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.: 217 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: BmdB-Cy2 was crystallized by mixing with 0.88% Tween 20, 1.62 M ammonium sulfate, 0.1 M HEPES pH 7.5, 2.67% PEG 400, and 3% 6-aminohexanoic acid, and equilibrated 0.88% Tween 20, 1.62 M ...Details: BmdB-Cy2 was crystallized by mixing with 0.88% Tween 20, 1.62 M ammonium sulfate, 0.1 M HEPES pH 7.5, 2.67% PEG 400, and 3% 6-aminohexanoic acid, and equilibrated 0.88% Tween 20, 1.62 M ammonium sulfate, 0.1 M HEPES pH 7.5, 2.67% PEG 400, and 3% 6-aminohexanoic acid. Crystals were transferred into a solution of mother liquor plus 20% (v/v) ethylene glycol, and flash-cooled in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→39.9 Å / Num. obs: 52064 / % possible obs: 99.8 % / Redundancy: 3.1 % / Net I/σ(I): 15.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JN3

4jn3


Resolution: 2.297→39.894 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 2623 5.04 %
Rwork0.2006 --
obs0.2024 52042 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.297→39.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7003 0 10 217 7230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047193
X-RAY DIFFRACTIONf_angle_d0.7739786
X-RAY DIFFRACTIONf_dihedral_angle_d17.9434318
X-RAY DIFFRACTIONf_chiral_restr0.051073
X-RAY DIFFRACTIONf_plane_restr0.0051272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2967-2.33840.32211190.29122338X-RAY DIFFRACTION91
2.3384-2.38340.37461160.2842616X-RAY DIFFRACTION100
2.3834-2.4320.29281440.27552586X-RAY DIFFRACTION100
2.432-2.48490.33111220.26582622X-RAY DIFFRACTION100
2.4849-2.54270.31011620.26092637X-RAY DIFFRACTION100
2.5427-2.60630.34561560.2582578X-RAY DIFFRACTION100
2.6063-2.67670.28831620.24682608X-RAY DIFFRACTION100
2.6767-2.75550.31131470.24632587X-RAY DIFFRACTION100
2.7555-2.84440.30931470.24242582X-RAY DIFFRACTION100
2.8444-2.9460.27271320.22672633X-RAY DIFFRACTION100
2.946-3.06390.26111310.23262594X-RAY DIFFRACTION100
3.0639-3.20330.29681260.22982649X-RAY DIFFRACTION100
3.2033-3.37210.27281420.22162629X-RAY DIFFRACTION100
3.3721-3.58330.22461270.20452633X-RAY DIFFRACTION100
3.5833-3.85970.21531410.18682611X-RAY DIFFRACTION100
3.8597-4.24780.21441360.17992615X-RAY DIFFRACTION100
4.2478-4.86150.19411470.16052624X-RAY DIFFRACTION99
4.8615-6.12140.21351390.17922608X-RAY DIFFRACTION99
6.1214-39.89990.18461270.17142669X-RAY DIFFRACTION98

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