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- PDB-8ejz: [4+2] Aza-Cyclase Y293F variant -

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Basic information

Entry
Database: PDB / ID: 8ejz
Title[4+2] Aza-Cyclase Y293F 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: 1.7 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
B: PbtD


Theoretical massNumber of molelcules
Total (without water)74,2002
Polymers74,2002
Non-polymers00
Water5,495305
1
A: PbtD


Theoretical massNumber of molelcules
Total (without water)37,1001
Polymers37,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PbtD


Theoretical massNumber of molelcules
Total (without water)37,1001
Polymers37,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.322, 88.734, 78.627
Angle α, β, γ (deg.)90.000, 91.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PbtD


Mass: 37099.793 Da / Num. of mol.: 2 / Mutation: Y293F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planobispora rosea (bacteria) / Gene: pbtD / Production host: Escherichia coli (E. coli) / References: UniProt: U5Q3T2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, pH = 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.068737 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.068737 Å / Relative weight: 1
ReflectionResolution: 1.696→78.598 Å / Num. obs: 61538 / % possible obs: 98 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.042 / Net I/σ(I): 14.1
Reflection shellResolution: 1.696→1.725 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 15518 / CC1/2: 0.72 / Rpim(I) all: 0.37 / % possible all: 87.2

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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: 1.7→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.371 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2941 4.8 %RANDOM
Rwork0.2069 ---
obs0.2082 58213 98.05 %-
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: 106.29 Å2 / Biso mean: 21.946 Å2 / Biso min: 9.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.36 Å2
2--0.38 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 0 305 5098
Biso mean---26.95 -
Num. residues----607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124920
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.6296686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.195605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.49318.774318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04315745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8771568
X-RAY DIFFRACTIONr_chiral_restr0.0830.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023872
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 224 -
Rwork0.288 3899 -
all-4123 -
obs--89.94 %

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