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- PDB-5wa4: Pyridine synthase, TbtD, from thiomuracin biosynthesis bound to a... -

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Basic information

Entry
Database: PDB / ID: 5wa4
TitlePyridine synthase, TbtD, from thiomuracin biosynthesis bound to an N-terminal leader peptide fragment
Components
  • Pyridine synthase TbtD
  • TbtA 16-mer peptide
KeywordsBIOSYNTHETIC PROTEIN / pyridine synthase / Diels-Alder / thiopeptide / thiomuracin
Function / homologyThiopeptide-type bacteriocin precursor / : / Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term / GE37468 family thiazolyl peptide / Thiopeptide-type bacteriocin biosynthesis domain-containing protein
Function and homology information
Biological speciesThermobispora bispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.646 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis.
Authors: Cogan, D.P. / Hudson, G.A. / Zhang, Z. / Pogorelov, T.V. / van der Donk, W.A. / Mitchell, D.A. / Nair, S.K.
History
DepositionJun 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Pyridine synthase TbtD
B: Pyridine synthase TbtD
C: Pyridine synthase TbtD
D: Pyridine synthase TbtD
E: Pyridine synthase TbtD
F: Pyridine synthase TbtD
M: TbtA 16-mer peptide
N: TbtA 16-mer peptide
O: TbtA 16-mer peptide
P: TbtA 16-mer peptide
Q: TbtA 16-mer peptide
R: TbtA 16-mer peptide


Theoretical massNumber of molelcules
Total (without water)252,87312
Polymers252,87312
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19100 Å2
ΔGint-93 kcal/mol
Surface area82340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.383, 105.998, 234.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pyridine synthase TbtD


Mass: 40320.555 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) (bacteria)
Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51
Gene: Tbis_0552 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D6Y504
#2: Protein/peptide
TbtA 16-mer peptide


Mass: 1825.023 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Thermobispora bispora (bacteria) / References: UniProt: D6Y501
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTbtD matches to NCBI Reference Sequence: WP_050760415.1

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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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M magnesium formate and 17.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07809 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07809 Å / Relative weight: 1
ReflectionResolution: 2.646→23.127 Å / Num. obs: 76366 / % possible obs: 98.9 % / Redundancy: 13.3 % / Net I/σ(I): 15.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W98

5w98


Resolution: 2.646→48.048 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 3728 4.89 %
Rwork0.2199 --
obs0.2232 76189 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.646→48.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15151 0 0 73 15224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115564
X-RAY DIFFRACTIONf_angle_d1.4321202
X-RAY DIFFRACTIONf_dihedral_angle_d16.3375674
X-RAY DIFFRACTIONf_chiral_restr0.0552315
X-RAY DIFFRACTIONf_plane_restr0.0092783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6462-2.67970.38381000.341994X-RAY DIFFRACTION92
2.6797-2.7150.42431360.33642474X-RAY DIFFRACTION95
2.715-2.75220.40411080.33282695X-RAY DIFFRACTION100
2.7522-2.79150.3941250.30112734X-RAY DIFFRACTION100
2.7915-2.83320.40351440.28022635X-RAY DIFFRACTION100
2.8332-2.87740.33521540.27862679X-RAY DIFFRACTION100
2.8774-2.92460.32371630.28282697X-RAY DIFFRACTION100
2.9246-2.9750.38391650.2832617X-RAY DIFFRACTION100
2.975-3.02910.33731310.2732738X-RAY DIFFRACTION100
3.0291-3.08740.35761230.27692714X-RAY DIFFRACTION100
3.0874-3.15040.32771260.26422676X-RAY DIFFRACTION100
3.1504-3.21880.37131250.26192733X-RAY DIFFRACTION100
3.2188-3.29370.32671540.25142695X-RAY DIFFRACTION100
3.2937-3.37610.291330.25172683X-RAY DIFFRACTION100
3.3761-3.46730.31841320.2492732X-RAY DIFFRACTION100
3.4673-3.56930.35861420.23932697X-RAY DIFFRACTION100
3.5693-3.68450.24921110.23042734X-RAY DIFFRACTION100
3.6845-3.81610.32761440.22982712X-RAY DIFFRACTION100
3.8161-3.96880.28651260.2222731X-RAY DIFFRACTION100
3.9688-4.14940.31011670.21252703X-RAY DIFFRACTION100
4.1494-4.3680.25311790.19672684X-RAY DIFFRACTION100
4.368-4.64150.28011110.18882782X-RAY DIFFRACTION100
4.6415-4.99950.27371170.1862764X-RAY DIFFRACTION100
4.9995-5.50190.25871580.1882734X-RAY DIFFRACTION100
5.5019-6.29660.27151610.20732764X-RAY DIFFRACTION100
6.2966-7.92730.24591330.1912820X-RAY DIFFRACTION100
7.9273-48.05620.19741600.15882840X-RAY DIFFRACTION97

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