[English] 日本語
Yorodumi
- PDB-1m9s: Crystal structure of Internalin B (InlB), a Listeria monocytogene... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m9s
TitleCrystal structure of Internalin B (InlB), a Listeria monocytogenes virulence protein containing SH3-like domains.
ComponentsInternalin B
KeywordsSIGNALING PROTEIN / internalin / cell invasion / GW domains / SH3 domains
Function / homology
Function and homology information


peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SH3 type barrels. - #170 / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent ...SH3 type barrels. - #170 / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Immunoglobulin-like - #1220 / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / SH3 type barrels. / Immunoglobulin E-set / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TERBIUM(III) ION / Internalin B / Internalin B
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsMarino, M. / Banerjee, M. / Jonquieres, R. / Cossart, P. / Ghosh, P.
CitationJournal: Embo J. / Year: 2002
Title: GW domains of the Listeria monocytogenes invasion protein InlB are SH3-like and mediate binding to host ligands
Authors: Marino, M. / Banerjee, M. / Jonquieres, R. / Cossart, P. / Ghosh, P.
History
DepositionJul 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Internalin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8319
Polymers68,6221
Non-polymers1,2098
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.5, 330.9, 182.4
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-643-

TB

DetailsThe biological assembly is a monomer composed of InlB residues 36 to 630. Residues 320 to 390 are present but disordered. Ambiguity in the position of this disordered region means that the monomer is made up of one N-terminal domain and one C-terminal domain, but there are two possible positions for the C-terminal domain. The alternate position for C-terminal domain is generated by the two fold axis (x = -x, y = y, z = 1/2 - z).

-
Components

#1: Protein Internalin B


Mass: 68622.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: inlB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25147, UniProt: P0DQD2*PLUS
#2: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 5.33 Å3/Da / Density % sol: 76.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: lithium sulfate, glycerol, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.9 M1reservoirLi2SO4
210 %glycerol1reservoir
31 mMdithiothreitol1reservoir
4100 mMMES1reservoirpH6.5

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.8455, 1.8461, 1.722
SYNCHROTRONNSLS X2521.6493, 1.6499, 1.61
SYNCHROTRONNSLS X2531.15
Detector
TypeIDDetectorDate
SBC-21CCDNov 21, 2000
ADSC QUANTUM 42CCDAug 3, 2001
ADSC QUANTUM 43CCDAug 3, 2001
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.84551
21.84611
31.7221
41.64931
51.64991
61.611
71.151
ReflectionResolution: 2.65→50 Å / Num. all: 43356 / Num. obs: 37423 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.4
Reflection shellResolution: 2.65→2.74 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.53 / % possible all: 59
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 59 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.5

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.65→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1706 -Random
Rwork0.273 ---
all0.274 43557 --
obs0.274 37408 85.8 %-
Displacement parametersBiso mean: 93.46 Å2
Baniso -1Baniso -2Baniso -3
1--11.353 Å20 Å20 Å2
2--27.901 Å20 Å2
3----16.547 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4170 0 12 65 4247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.344
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_dihedral_angle_d24.743
X-RAY DIFFRACTIONc_improper_angle_d1.068
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.274 / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.743
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.068
LS refinement shell
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 2.74 Å / Rfactor Rfree: 0.488 / Rfactor Rwork: 0.46

+
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