[English] 日本語
Yorodumi
- PDB-7qeh: LTA-binding domain of SlpA, the S-layer protein from Lactobacillu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qeh
TitleLTA-binding domain of SlpA, the S-layer protein from Lactobacillus amylovorus
ComponentsS-layer
KeywordsCELL ADHESION / s-layer / LTA-binding / lactobacillus amylovorus / polymer binding
Function / homologyLactobacillus surface layer protein / Surface layer protein A domain / Surface layer protein A domain / structural constituent of cell wall / S-layer / peptidoglycan-based cell wall / PHOSPHATE ION / S-layer
Function and homology information
Biological speciesLactobacillus amylovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å
AuthorsEder, M. / Dordic, A. / Sagmeister, T. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP29432 Austria
CitationJournal: to be published
Title: The binding of the lactobacilli S-layer protein to the bacterial cell through interaction with LTA
Authors: Eder, M. / Gubensaek, N. / Sagmeister, T. / Grininger, C. / Vejzovic, D. / Damisch, E. / Dordic, A. / Codee, J. / Pavkov-Keller, T.
History
DepositionDec 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-layer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3272
Polymers16,2321
Non-polymers951
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.561, 43.481, 89.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein S-layer /


Mass: 16231.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus amylovorus (strain GRL 1112) (bacteria)
Strain: GRL 1112 / Gene: LA2_00970 / Production host: Escherichia coli (E. coli) / References: UniProt: E4SK47
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus screen condition #2-29 (20 mM of each carboxylic acid (sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate, and sodium ...Details: Morpheus screen condition #2-29 (20 mM of each carboxylic acid (sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate, and sodium oxamate), 0.1 M sodium HEPES- MOPS pH 7.5 with 20 % v/v PEG 500 MME and 10 % w/v PEG 20000). A protein stock solution of 20 mg/mL in 10 mM HEPES pH 7 and 100 mM NaCl was used. 1uL drop with 1:1 ration protein to reservoir solution.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.67→39.08 Å / Num. obs: 26186 / % possible obs: 99.39 % / Redundancy: 12.2 % / Biso Wilson estimate: 18.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.114 / Net I/σ(I): 19.84
Reflection shellResolution: 1.67→1.734 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1361 / CC1/2: 0.805 / CC star: 0.947 / Rpim(I) all: 0.316

-
Processing

Software
NameVersionClassification
XDSdata reduction
SHELXCDphasing
SHELXEmodel building
PHENIX1.16_3549refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.67→39.08 Å / SU ML: 0.1598 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1904 2612 9.98 %
Rwork0.1626 23573 -
obs0.1655 26185 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.47 Å2
Refinement stepCycle: LAST / Resolution: 1.67→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 5 75 1045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091994
X-RAY DIFFRACTIONf_angle_d0.99831336
X-RAY DIFFRACTIONf_chiral_restr0.0666150
X-RAY DIFFRACTIONf_plane_restr0.0056164
X-RAY DIFFRACTIONf_dihedral_angle_d12.928603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.27561230.27521079X-RAY DIFFRACTION85.31
1.71-1.740.20841430.19921235X-RAY DIFFRACTION99.93
1.74-1.770.23591360.19111253X-RAY DIFFRACTION99.86
1.77-1.810.22631410.17521236X-RAY DIFFRACTION99.78
1.81-1.850.24541350.17551237X-RAY DIFFRACTION100
1.85-1.90.21971450.16611273X-RAY DIFFRACTION100
1.9-1.950.24291330.15961231X-RAY DIFFRACTION100
1.95-2.010.16841420.16271263X-RAY DIFFRACTION100
2.01-2.070.18021310.14791266X-RAY DIFFRACTION100
2.07-2.150.24611340.16451247X-RAY DIFFRACTION99.93
2.15-2.230.1881350.14761249X-RAY DIFFRACTION99.93
2.23-2.340.18251400.16031259X-RAY DIFFRACTION100
2.34-2.460.2031420.15871233X-RAY DIFFRACTION100
2.46-2.610.19851380.17661254X-RAY DIFFRACTION100
2.61-2.810.18851410.16911265X-RAY DIFFRACTION100
2.81-3.10.19111400.17161255X-RAY DIFFRACTION100
3.1-3.550.18161300.15041241X-RAY DIFFRACTION99.71
3.55-4.470.15591410.1411264X-RAY DIFFRACTION99.93
4.47-39.080.17831420.16761233X-RAY DIFFRACTION100

+
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