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- PDB-5w98: Pyridine synthase, PbtD, from GE2270 biosynthesis -

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Basic information

Entry
Database: PDB / ID: 5w98
TitlePyridine synthase, PbtD, from GE2270 biosynthesis
ComponentsPbtD
KeywordsBIOSYNTHETIC PROTEIN / pyridine synthase / Diels-Alder
Function / homology: / Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term / PbtD
Function and homology information
Biological speciesPlanobispora rosea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å
AuthorsCogan, D.P. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM079038-07 United States
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 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PbtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5422
Polymers37,3471
Non-polymers1951
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.247, 88.132, 44.473
Angle α, β, γ (deg.)90.00, 109.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PbtD


Mass: 37347.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planobispora rosea (bacteria) / Gene: pbtD / Plasmid: pRARE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: U5Q3T2
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% MPD, 8% PEG 6K, 0.1 M MES 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: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.227→44.1 Å / Num. obs: 90136 / % possible obs: 96.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.9
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2.2 / Rpim(I) all: 0.368 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.23→44.07 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.667 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18617 4320 4.8 %RANDOM
Rwork0.16249 ---
obs0.16363 85777 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.22 Å2
2---0.82 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.23→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 12 370 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192535
X-RAY DIFFRACTIONr_bond_other_d0.0020.022338
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.9413458
X-RAY DIFFRACTIONr_angle_other_deg1.14135359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80621.2125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47415386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3991534
X-RAY DIFFRACTIONr_chiral_restr0.260.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022911
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02608
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_it1.6431.4611252
X-RAY DIFFRACTIONr_mcbond_other1.6431.4581251
X-RAY DIFFRACTIONr_mcangle_it2.4162.1861579
X-RAY DIFFRACTIONr_mcangle_other2.4162.1881580
X-RAY DIFFRACTIONr_scbond_it2.8581.8171283
X-RAY DIFFRACTIONr_scbond_other2.8571.8171283
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2132.6161880
X-RAY DIFFRACTIONr_long_range_B_refined6.06119.8913089
X-RAY DIFFRACTIONr_long_range_B_other5.54818.4782940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.227→1.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 305 -
Rwork0.278 5713 -
obs--87.67 %

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