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- PDB-6gkw: Crystal structure of the R-type bacteriocin sheath protein CD1363... -

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Basic information

Entry
Database: PDB / ID: 6gkw
TitleCrystal structure of the R-type bacteriocin sheath protein CD1363 from Clostridium difficile in the pre-assembled state
ComponentsPutative phage XkdK-like protein
KeywordsSTRUCTURAL PROTEIN / Diffocin Sheath
Function / homologyTail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Phage XkdK-like protein
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSchwemmlein, N. / Pippel, J. / Gazdag, E.M. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Volkswagen FoundationVWZN2889/3215/3266. Germany
CitationJournal: Front Microbiol / Year: 2018
Title: Crystal Structures of R-Type Bacteriocin Sheath and Tube Proteins CD1363 and CD1364 FromClostridium difficilein the Pre-assembled State.
Authors: Schwemmlein, N. / Pippel, J. / Gazdag, E.M. / Blankenfeldt, W.
History
DepositionMay 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phage XkdK-like protein


Theoretical massNumber of molelcules
Total (without water)39,7701
Polymers39,7701
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.935, 47.878, 112.500
Angle α, β, γ (deg.)90.000, 92.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative phage XkdK-like protein


Mass: 39769.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: CD630_13630 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18BN0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Lithium chloride, 0.1 M Tris pH 8.0, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→40.49 Å / Num. obs: 32088 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 33.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Net I/σ(I): 21.5
Reflection shell

Diffraction-ID: 1 / Redundancy: 13.3 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.941.50720870.7260.4211.56699.8
9.11-40.490.043160.9990.0110.04299.1

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
PHENIXdev_3112refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.352 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.1
RfactorNum. reflection% reflection
Rfree0.2485 1671 5.21 %
Rwork0.2131 --
obs0.2149 32078 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.67 Å2 / Biso mean: 56.5317 Å2 / Biso min: 20.28 Å2
Refinement stepCycle: final / Resolution: 1.9→38.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 0 180 2877
Biso mean---45.59 -
Num. residues----351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9560.36221500.316625082658100
1.956-2.01910.27861300.2962488261899
2.0191-2.09120.34121370.281825202657100
2.0912-2.1750.29731380.252925292667100
2.175-2.27390.25921570.235724792636100
2.2739-2.39380.27121340.230325452679100
2.3938-2.54380.27521430.228225132656100
2.5438-2.74010.28421230.237125262649100
2.7401-3.01580.2691520.228525412693100
3.0158-3.45190.24661370.220725642701100
3.4519-4.34810.21431470.179125412688100
4.3481-38.35940.21631230.182726532776100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90430.3054-0.75451.4809-1.24733.466-0.354-1.8557-0.23070.2417-0.0993-0.06830.37140.57450.02970.42810.0168-0.02741.1198-0.02630.357311.4873-1.628336.6958
26.46431.3831-0.37382.8273-0.20971.860.1271-1.33520.98750.1987-0.08710.25320.02280.06240.05560.3284-0.04280.01170.561-0.25470.4101-3.57433.660232.8582
32.34391.1067-0.46613.3492-0.00494.6643-0.125-0.0207-0.1135-0.15870.02420.19460.2015-0.33380.03760.2412-0.0145-0.03010.1299-0.01820.172717.41959.65312.2625
43.3898-0.8754-0.3374.3660.46910.2119-0.29370.09390.39770.1458-0.2463-0.011-1.4324-0.04140.41470.80040.0076-0.05780.23960.01760.326819.092127.06892.7216
54.32514.78850.0656.4088-0.48122.93570.046-0.13590.2249-0.1410.03180.84410.242-0.54840.01510.3076-0.038-0.01820.28610.00940.40768.60379.94512.3789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 61 )A4 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 248 )A62 - 248
3X-RAY DIFFRACTION3chain 'A' and (resid 249 through 311 )A249 - 311
4X-RAY DIFFRACTION4chain 'A' and (resid 312 through 328 )A312 - 328
5X-RAY DIFFRACTION5chain 'A' and (resid 329 through 354)A329 - 354

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