[English] 日本語
Yorodumi
- PDB-6gkw: Crystal structure of the R-type bacteriocin sheath protein CD1363... -

+
Open data


ID or keywords:

Loading...

-
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
Revision 1.2Nov 6, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more