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- PDB-8t19: RiPP precursor peptide recognition element (RRE) domain of Ocin-T... -

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Basic information

Entry
Database: PDB / ID: 8t19
TitleRiPP precursor peptide recognition element (RRE) domain of Ocin-ThiF-like partner protein, PbtF, bound to an 8 residue fragment of its precursor peptide, PbtA
Components
  • PbtA
  • PbtF
KeywordsBIOSYNTHETIC PROTEIN / peptide binding protein
Function / homologyThiopeptide-type bacteriocin precursor / PbtA / PbtF
Function and homology information
Biological speciesPlanobispora rosea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å
AuthorsCogan, D.P. / Nair, S.K. / Mitchell, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM097142-11S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3R01GM079038-12S1 United States
CitationJournal: To Be Published
Title: Discovery and validation of RRE domains
Authors: Shelton, K.E. / Bregman, M. / Cogan, D.P. / Nair, S.K. / Mitchell, D.A.
History
DepositionJun 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PbtF
B: PbtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0833
Polymers15,0582
Non-polymers241
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area5440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.259, 40.259, 101.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

21A-290-

HOH

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Components

#1: Protein PbtF


Mass: 9318.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planobispora rosea (bacteria) / Gene: pbtF, Pro02_44330 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U5Q0A7
#2: Protein PbtA


Mass: 5739.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Planobispora rosea (bacteria) / References: UniProt: U5Q0A5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.58 Å3/Da / Density % sol: 22.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 27.5% PEG 3350, 0.2 M MgCl2, 0.1 M tris pH 8.0 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.23→32.99 Å / Num. obs: 28683 / % possible obs: 99.76 % / Redundancy: 2 % / Biso Wilson estimate: 15.51 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01201 / Rpim(I) all: 0.01201 / Rrim(I) all: 0.01698 / Net I/σ(I): 24.06
Reflection shellResolution: 1.23→1.274 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2323 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 2805 / CC1/2: 0.881 / CC star: 0.968 / Rpim(I) all: 0.2323 / Rrim(I) all: 0.3286 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.23→32.99 Å / SU ML: 0.1259 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.7422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 1467 5.11 %
Rwork0.2212 27216 -
obs0.223 28683 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.55 Å2
Refinement stepCycle: LAST / Resolution: 1.23→32.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms705 0 1 104 810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061731
X-RAY DIFFRACTIONf_angle_d0.8971999
X-RAY DIFFRACTIONf_chiral_restr0.0777120
X-RAY DIFFRACTIONf_plane_restr0.0071127
X-RAY DIFFRACTIONf_dihedral_angle_d12.5488259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.270.32451570.26832650X-RAY DIFFRACTION100
1.27-1.320.28251240.25862690X-RAY DIFFRACTION99.93
1.32-1.380.2721490.24372704X-RAY DIFFRACTION99.96
1.38-1.460.26621430.22642672X-RAY DIFFRACTION100
1.46-1.550.2411560.23092704X-RAY DIFFRACTION100
1.55-1.670.25581260.21352716X-RAY DIFFRACTION99.96
1.67-1.830.26521380.22922736X-RAY DIFFRACTION100
1.83-2.10.22311640.21322715X-RAY DIFFRACTION100
2.1-2.650.23841480.22442768X-RAY DIFFRACTION100
2.65-32.990.26721620.21372861X-RAY DIFFRACTION97.99

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