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- PDB-8ejy: [4+2] Aza-Cyclase F293A variant -

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Basic information

Entry
Database: PDB / ID: 8ejy
Title[4+2] Aza-Cyclase F293A variant
ComponentsPbtD
KeywordsANTIBIOTIC / Enzyme / thiopeptide / RiPP / biosynthesis.
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 / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsNair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131347 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Enzymatic Pyridine Aromatization during Thiopeptide Biosynthesis.
Authors: Rice, A.J. / Pelton, J.M. / Kramer, N.J. / Catlin, D.S. / Nair, S.K. / Pogorelov, T.V. / Mitchell, D.A. / Bowers, A.A.
History
DepositionSep 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PbtD


Theoretical massNumber of molelcules
Total (without water)37,0811
Polymers37,0811
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.524, 79.567, 82.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PbtD


Mass: 37080.754 Da / Num. of mol.: 1 / Mutation: Y293A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planobispora rosea (bacteria) / Gene: pbtD / Variant: F293A / Production host: Escherichia coli (E. coli) / References: UniProt: U5Q3T2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, pH = 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.47→100 Å / Num. obs: 14813 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 14.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.03 / Rrim(I) all: 0.114 / Net I/σ(I): 18.9
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.406 / Num. unique obs: 735 / CC1/2: 0.714 / Rpim(I) all: 0.376 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w98

5w98


Resolution: 2.47→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.287 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 719 4.9 %RANDOM
Rwork0.2073 ---
obs0.2097 14067 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 130.74 Å2 / Biso mean: 61.803 Å2 / Biso min: 27.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--2.12 Å2-0 Å2
3----2.48 Å2
Refinement stepCycle: final / Resolution: 2.47→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 0 26 2414
Biso mean---52.26 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122448
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.6283325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23318.581155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31515370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5971534
X-RAY DIFFRACTIONr_chiral_restr0.0960.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021920
LS refinement shellResolution: 2.47→2.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 51 -
Rwork0.302 1013 -
all-1064 -
obs--100 %

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