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- PDB-6gkx: Crystal structure of the R-type bacteriocin tube protein CD1364 f... -

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Basic information

Entry
Database: PDB / ID: 6gkx
TitleCrystal structure of the R-type bacteriocin tube protein CD1364 from Clostridium difficile in the pre-assembled state
ComponentsPutative phage XkdM-like protein
KeywordsSTRUCTURAL PROTEIN / Diffocin Tube
Function / homologyPhage tail tube protein / XkdM-like superfamily / Phage tail tube protein / Phage XkdM-like protein
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Putative phage XkdM-like protein


Theoretical massNumber of molelcules
Total (without water)16,3141
Polymers16,3141
Non-polymers00
Water2,324129
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 area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.323, 36.323, 216.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative phage XkdM-like protein


Mass: 16313.716 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_13640 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18BM9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M ammoniumchloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.5→43.36 Å / Num. obs: 24715 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 23.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.017 / Rrim(I) all: 0.085 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.5325.92.2911940.7040.4552.335100
8.22-43.3617.40.04122710.010.04299.8

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
PHENIXdev_3112refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUJ

2guj


Resolution: 1.5→35.824 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.94
RfactorNum. reflection% reflection
Rfree0.22 1177 4.79 %
Rwork0.1915 --
obs0.1928 24596 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.24 Å2 / Biso mean: 40.8498 Å2 / Biso min: 16.25 Å2
Refinement stepCycle: final / Resolution: 1.5→35.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 0 129 1160
Biso mean---38.3 -
Num. residues----134
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.56830.30951300.267828392969
1.5683-1.6510.29891470.234428793026
1.651-1.75440.26791440.217328252969
1.7544-1.88980.2381510.197128933044
1.8898-2.080.21011400.183928903030
2.08-2.38090.23321730.179828963069
2.3809-2.99950.21621540.195729813135
2.9995-35.8340.20221380.184532163354
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)
14.44120.51051.11381.6394-0.25545.6552-0.1415-0.20210.12260.25460.1326-0.1076-0.1550.5151-0.05570.23860.0672-0.04710.2021-0.04780.24138.492622.267792.1791
24.25751.57192.2256.00233.79015.9575-0.1212-0.0711-0.14620.25660.3236-0.3367-0.01530.3831-0.21840.1840.0491-0.02850.18130.01940.20437.880425.137990.8252
37.3893-5.5325-6.53045.96035.38496.58030.55340.1655-0.1889-0.8182-0.8070.6787-0.3084-0.92920.29740.38930.113-0.00670.7152-0.03050.247620.544630.6596109.6565
46.6307-1.2292-0.73415.35342.92534.56220.03090.3235-0.312-0.05350.1177-0.27060.29130.3954-0.15230.1313-0.02370.01940.1824-0.00340.203437.835926.136983.0302
54.7474-4.5232-4.79584.49374.36718.28020.55430.1412-0.0637-0.3686-0.08430.2334-0.58260.1299-0.46030.28680.0069-0.0260.19030.00480.222624.654427.537175.2204
69.3164-5.20266.40586.6333-4.57736.85020.03320.1543-0.32970.14940.12980.13610.11640.2683-0.13790.17650.01470.01260.1567-0.02140.150330.607323.781887.3465
72.0891-0.69310.18173.8298-1.66074.36370.0287-0.03760.03910.25040.0519-0.26770.12640.41930.01950.17650.0325-0.04320.2066-0.05110.190736.880924.515991.1959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 21 )A7 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 35 )A22 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 56 )A36 - 56
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 70 )A57 - 70
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 81 )A71 - 81
6X-RAY DIFFRACTION6chain 'A' and (resid 82 through 92 )A82 - 92
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 142 )A93 - 142

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