[English] 日本語
Yorodumi
- PDB-5x1e: Structure of DotL(656-783)-IcmS-IcmW derived from Legionella pneu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x1e
TitleStructure of DotL(656-783)-IcmS-IcmW derived from Legionella pneumophila
Components
  • (IcmO (DotL)) x 2
  • (IcmS) x 2
  • IcmW
KeywordsPROTEIN TRANSPORT / type IV secretion system / Coupling protein complex / Effector translocation
Function / homology
Function and homology information


protein transport / plasma membrane / cytoplasm
Similarity search - Function
Type IVb secretion, IcmS, effector-recruitment / : / Type IVb secretion, IcmS, effector-recruitment / TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 4 adapter protein IcmW / Type 4 coupling protein DotL / Type 4 adapter protein IcmS
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.999 Å
AuthorsKim, J.D. / Kwak, M.J. / Oh, B.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF)2008-0061987 Korea, Republic Of
CitationJournal: Nat Microbiol / Year: 2017
Title: Architecture of the type IV coupling protein complex of Legionella pneumophila
Authors: Kwak, M.J. / Kim, J.D. / Kim, H. / Kim, C. / Bowman, J.W. / Kim, S. / Joo, K. / Lee, J. / Jin, K.S. / Kim, Y.G. / Lee, N.K. / Jung, J.U. / Oh, B.H.
History
DepositionJan 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IcmS
B: IcmW
C: IcmO (DotL)
D: IcmS
E: IcmW
F: IcmO (DotL)


Theoretical massNumber of molelcules
Total (without water)80,9066
Polymers80,9066
Non-polymers00
Water2,270126
1
A: IcmS
B: IcmW
C: IcmO (DotL)


Theoretical massNumber of molelcules
Total (without water)40,4883
Polymers40,4883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-70 kcal/mol
Surface area16910 Å2
MethodPISA
2
D: IcmS
E: IcmW
F: IcmO (DotL)


Theoretical massNumber of molelcules
Total (without water)40,4173
Polymers40,4173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-67 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.597, 75.803, 150.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 5 types, 6 molecules ABECDF

#1: Protein IcmS


Mass: 12149.954 Da / Num. of mol.: 1 / Fragment: UNP residues 5-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: icmS, lpg0442 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYD0
#2: Protein IcmW


Mass: 16974.447 Da / Num. of mol.: 2 / Fragment: UNP residues 2-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: icmW, lpg2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZS31
#3: Protein IcmO (DotL)


Mass: 11363.930 Da / Num. of mol.: 1 / Fragment: UNP residues 672-773
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: icmO, lpg0446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYC6
#4: Protein IcmS


Mass: 12265.042 Da / Num. of mol.: 1 / Fragment: UNP residues 4-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: icmS, lpg0442 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYD0
#5: Protein IcmO (DotL)


Mass: 11177.764 Da / Num. of mol.: 1 / Fragment: UNP residues 674-773
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: icmO, lpg0446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYC6

-
Non-polymers , 1 types, 126 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.24 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25%(v/v) PEG550 monoethylether, 100mM MES (pH 6.5), 10mM zinc sulfate and 5mM spermine tetrahydrochloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 97546 / % possible obs: 92 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.37 Å2 / Rmerge(I) obs: 0.1 / Χ2: 4.875 / Net I/σ(I): 16.7 / Num. measured all: 262793
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.10.28922281.496185.5
2.03-2.073.40.25922941.461187.8
2.07-2.113.70.23323731.507190.1
2.11-2.1540.21723661.607190.8
2.15-2.23.80.19722611.658187.5
2.2-2.253.80.221180310.981168.5
2.25-2.313.60.19617403.533167
2.31-2.374.90.1624492.054193.3
2.37-2.445.20.15125062.232195.3
2.44-2.525.40.14825122.547195.3
2.52-2.615.70.1325472.762196.8
2.61-2.715.90.12525783.008197.6
2.71-2.846.10.11925653.628197.5
2.84-2.996.40.11125844.187198.2
2.99-3.176.60.10826355.363198.8
3.17-3.426.50.09926256.219198.6
3.42-3.765.70.09325787.056196
3.76-4.316.60.07625657.104195.7
4.31-5.437.40.06927147.422199.4
5.43-507.50.074285010.344198.9

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.999→36.756 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.72 / Phase error: 23.21 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.269 3529 4.08 %
Rwork0.2213 82965 -
obs0.2231 86494 85.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.84 Å2 / Biso mean: 23.0888 Å2 / Biso min: 4.43 Å2
Refinement stepCycle: final / Resolution: 1.999→36.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5371 0 0 126 5497
Biso mean---20.83 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085458
X-RAY DIFFRACTIONf_angle_d0.9727407
X-RAY DIFFRACTIONf_chiral_restr0.051877
X-RAY DIFFRACTIONf_plane_restr0.006957
X-RAY DIFFRACTIONf_dihedral_angle_d13.1863320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9988-2.02620.27931020.26122281238360
2.0262-2.05510.28811220.25622895301774
2.0551-2.08580.31191300.25952975310577
2.0858-2.11840.30881280.24983091321979
2.1184-2.15310.3091340.25153083321780
2.1531-2.19020.27591340.24573082321680
2.1902-2.230.281830.27691934201750
2.23-2.27290.5121070.45772591269867
2.2729-2.31930.2543980.26412384248262
2.3193-2.36970.331450.21243409355488
2.3697-2.42480.24781430.20643496363989
2.4248-2.48550.28531520.21133504365691
2.4855-2.55270.20131540.2063539369391
2.5527-2.62780.29131540.20543639379394
2.6278-2.71250.28451490.2163654380394
2.7125-2.80950.25691620.21863698386094
2.8095-2.92190.271580.22283722388096
2.9219-3.05480.28311620.22993727388996
3.0548-3.21580.28841630.22753755391898
3.2158-3.41710.27481650.23073789395497
3.4171-3.68080.26531480.22163604375293
3.6808-4.05070.22451430.18243573371692
4.0507-4.63590.20191610.16443830399199
4.6359-5.8370.23571670.18613852401999
5.837-36.76210.2291650.18363858402399

+
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