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- PDB-5civ: Sibling Lethal Factor Precursor - DfsB -

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Basic information

Entry
Database: PDB / ID: 5civ
TitleSibling Lethal Factor Precursor - DfsB
ComponentsSibling bacteriocin
KeywordsUNKNOWN FUNCTION / Bacteriocin / sporulation / DUF1706 / cell cycle
Function / homologyProtein of unknown function DUF1706 / Protein of unknown function (DUF1706) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Sibling bacteriocin
Function and homology information
Biological speciesPaenibacillus dendritiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.384 Å
AuthorsTaylor, J.D. / Matthews, S.J.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide.
Authors: Taylor, J.D. / Taylor, G. / Hare, S.A. / Matthews, S.J.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sibling bacteriocin


Theoretical massNumber of molelcules
Total (without water)21,8681
Polymers21,8681
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.590, 47.680, 72.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sibling bacteriocin


Mass: 21868.219 Da / Num. of mol.: 1 / Fragment: residues 13-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus dendritiformis (bacteria)
Gene: dfsB / Plasmid: pQE-30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0EVD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12% PEG 550 MME, 6% PEG 20,000, 0.1 M Sodium formate; 0.1 M Ammonium acetate; 0.1 M Sodium citrate tribasic dihydrate; 0.1 M Sodium potassium tartrate tetrahydrate; 0.1 M Sodium oxamate, 0.1 M Tris, 0.1 M Bicine
PH range: 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2011
RadiationMonochromator: 0.9788 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.38→21.51 Å / Num. obs: 32427 / % possible obs: 94.72 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 17.4
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 4.4 % / % possible all: 74.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.384→21.509 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.74 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1988 1967 6.07 %
Rwork0.1814 --
obs0.1824 32427 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.384→21.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 0 238 1654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061458
X-RAY DIFFRACTIONf_angle_d1.0221977
X-RAY DIFFRACTIONf_dihedral_angle_d13.958540
X-RAY DIFFRACTIONf_chiral_restr0.042200
X-RAY DIFFRACTIONf_plane_restr0.006252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3843-1.41890.2757960.27741523X-RAY DIFFRACTION67
1.4189-1.45720.25841220.26181824X-RAY DIFFRACTION81
1.4572-1.50010.23241360.21512168X-RAY DIFFRACTION95
1.5001-1.54850.21581400.20432179X-RAY DIFFRACTION96
1.5485-1.60380.22261450.19312198X-RAY DIFFRACTION97
1.6038-1.6680.21461430.1892203X-RAY DIFFRACTION98
1.668-1.74390.20491430.18782226X-RAY DIFFRACTION98
1.7439-1.83580.23751430.19332258X-RAY DIFFRACTION98
1.8358-1.95080.20931440.18422241X-RAY DIFFRACTION99
1.9508-2.10130.18591450.17742269X-RAY DIFFRACTION99
2.1013-2.31250.19571500.16762270X-RAY DIFFRACTION99
2.3125-2.64660.23361500.1782324X-RAY DIFFRACTION100
2.6466-3.33240.16891510.18152338X-RAY DIFFRACTION100
3.3324-21.51120.17461590.16352439X-RAY DIFFRACTION99

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