[English] 日本語
Yorodumi
- PDB-7ym7: Crystal structure of the Salmonella effector SseK1 F187A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ym7
TitleCrystal structure of the Salmonella effector SseK1 F187A mutant
ComponentsType III secretion system effector arginine glycosyltransferase SseK1
KeywordsTOXIN / salmonella / effector / arginine glycosylation
Function / homologytransferase activity / Type III secretion system effector arginine glycosyltransferase SseK1
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, U.J. / Park, J.B. / Yoo, Y. / Cho, H.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of the Salmonella effector SseK1
Authors: Kim, U.J. / Park, J.B. / Yoo, Y. / Cho, H.S.
History
DepositionJul 27, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 2, 2023ID: 6IXK
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type III secretion system effector arginine glycosyltransferase SseK1
B: Type III secretion system effector arginine glycosyltransferase SseK1


Theoretical massNumber of molelcules
Total (without water)70,2152
Polymers70,2152
Non-polymers00
Water724
1
A: Type III secretion system effector arginine glycosyltransferase SseK1


Theoretical massNumber of molelcules
Total (without water)35,1081
Polymers35,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III secretion system effector arginine glycosyltransferase SseK1


Theoretical massNumber of molelcules
Total (without water)35,1081
Polymers35,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.380, 47.760, 81.780
Angle α, β, γ (deg.)90.000, 97.930, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Type III secretion system effector arginine glycosyltransferase SseK1


Mass: 35107.641 Da / Num. of mol.: 2 / Mutation: F187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: G3V45_004211, G4O83_004375, G4X61_004300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A735ZBM9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate 0.1 M MES:NaOH pH 6.5 30% (w/v) PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.09 Å / Num. obs: 34504 / % possible obs: 98.73 % / Redundancy: 5.2 % / Biso Wilson estimate: 49.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06397 / Rpim(I) all: 0.03048 / Rrim(I) all: 0.07112 / Net I/σ(I): 15.03
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 3381 / CC1/2: 0.819 / CC star: 0.949 / Rpim(I) all: 0.577 / Rrim(I) all: 0.07112 / % possible all: 97.77

-
Processing

Software
NameVersionClassification
REFMACv1.0refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.09 Å / SU ML: 0.3928 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.4251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2671 1709 4.96 %
Rwork0.2417 32748 -
obs0.2429 34457 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 0 4 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01254900
X-RAY DIFFRACTIONf_angle_d1.60166598
X-RAY DIFFRACTIONf_chiral_restr0.0878695
X-RAY DIFFRACTIONf_plane_restr0.0064865
X-RAY DIFFRACTIONf_dihedral_angle_d15.89531836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.41731220.36932678X-RAY DIFFRACTION97.87
2.26-2.340.38441490.33982707X-RAY DIFFRACTION98.18
2.34-2.420.36861310.33122699X-RAY DIFFRACTION98.5
2.42-2.520.36091350.30972702X-RAY DIFFRACTION98.75
2.52-2.630.32011450.30612712X-RAY DIFFRACTION98.59
2.63-2.770.32071590.31392680X-RAY DIFFRACTION98.51
2.77-2.950.2941600.27842708X-RAY DIFFRACTION98.93
2.95-3.170.28841590.2632713X-RAY DIFFRACTION98.83
3.17-3.490.30741380.26062729X-RAY DIFFRACTION99.2
3.49-40.26251450.22922743X-RAY DIFFRACTION98.67
4-5.030.21281350.19382790X-RAY DIFFRACTION99.39
5.04-46.090.20841310.20482887X-RAY DIFFRACTION99.44

+
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://pdbjlvh1.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