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- PDB-5wa3: Pyridine synthase, TbtD, from thiomuracin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 5wa3
TitlePyridine synthase, TbtD, from thiomuracin biosynthesis
ComponentsPyridine synthase TbtD
KeywordsBIOSYNTHETIC PROTEIN / pyridine synthase / Diels-Alder / thiopeptide / thiomuracin
Function / homology: / Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term / Thiopeptide-type bacteriocin biosynthesis domain-containing protein
Function and homology information
Biological speciesThermobispora bispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

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Assembly

Deposited unit
A: Pyridine synthase TbtD
B: Pyridine synthase TbtD


Theoretical massNumber of molelcules
Total (without water)80,6412
Polymers80,6412
Non-polymers00
Water00
1
A: Pyridine synthase TbtD


Theoretical massNumber of molelcules
Total (without water)40,3211
Polymers40,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyridine synthase TbtD


Theoretical massNumber of molelcules
Total (without water)40,3211
Polymers40,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Pyridine synthase TbtD
B: Pyridine synthase TbtD

A: Pyridine synthase TbtD
B: Pyridine synthase TbtD

A: Pyridine synthase TbtD
B: Pyridine synthase TbtD


Theoretical massNumber of molelcules
Total (without water)241,9236
Polymers241,9236
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11690 Å2
ΔGint-34 kcal/mol
Surface area82010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.830, 155.830, 165.239
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Pyridine synthase TbtD


Mass: 40320.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobispora bispora (bacteria)
Strain: ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51
Gene: Tbis_0552 / Plasmid: pRARE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D6Y504
Sequence detailsTbtD in the NCBI database: 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: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.4 M NaH2PO4, 1 M KH2PO4 pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→55.08 Å / Num. obs: 34569 / % possible obs: 93.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W98

5w98


Resolution: 2.8→104.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.451 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24167 1729 5 %RANDOM
Rwork0.19748 ---
obs0.19967 32840 93.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.8→104.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 0 0 4874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195007
X-RAY DIFFRACTIONr_bond_other_d0.0020.024663
X-RAY DIFFRACTIONr_angle_refined_deg1.871.956822
X-RAY DIFFRACTIONr_angle_other_deg1.179310655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8095612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69220.453243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.01115748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4861574
X-RAY DIFFRACTIONr_chiral_restr0.1030.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215651
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021187
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.8938.8162460
X-RAY DIFFRACTIONr_mcbond_other7.8878.8152459
X-RAY DIFFRACTIONr_mcangle_it11.36413.1923068
X-RAY DIFFRACTIONr_mcangle_other11.36313.1943069
X-RAY DIFFRACTIONr_scbond_it7.7139.1322547
X-RAY DIFFRACTIONr_scbond_other7.7129.1332548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.13813.4973755
X-RAY DIFFRACTIONr_long_range_B_refined14.2745585
X-RAY DIFFRACTIONr_long_range_B_other14.2735586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 142 -
Rwork0.323 2600 -
obs--100 %

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