[English] 日本語
Yorodumi
- PDB-9qr5: InlB392_V333E: V333E variant of Listeria monocytogenes InlB (inte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qr5
TitleInlB392_V333E: V333E variant of Listeria monocytogenes InlB (internalin B) residues 36-392
ComponentsInternalin B
KeywordsCELL INVASION / LEUCINE RICH REPEAT / PROTEIN BINDING / PATHOGENICITY / VIRULENCE FACTOR
Function / homology
Function and homology information


peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
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 ...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 / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGeerds, C. / Niemann, H.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Single mutations to tyrosine or glutamate improve crystallizability and crystal diffraction properties of a flexible two-domain protein
Authors: Geerds, C. / Niemann, H.H.
History
DepositionApr 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Internalin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7284
Polymers40,4521
Non-polymers2763
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-2 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.410, 90.770, 99.120
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 Internalin B / InlB / Invasion protein InlB


Mass: 40451.773 Da / Num. of mol.: 1 / Mutation: V333E
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GPLGS remain after proteolytic removal of the expression tag point mutation V333E
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: inlB, lmo0434 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: P0DQD2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 % / Description: size about 90 x 20 x 20 micrometer
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Reservoir solution: PEG Smear Screen Medium Molecular Weight, Condition E1: 0.1 M HEPES pH 7.5, 22.5% PEG medium molecular weight (MMW) mixture consisting of PEG1500, PEG2000, PEG2000MME, ...Details: Reservoir solution: PEG Smear Screen Medium Molecular Weight, Condition E1: 0.1 M HEPES pH 7.5, 22.5% PEG medium molecular weight (MMW) mixture consisting of PEG1500, PEG2000, PEG2000MME, PEG3000, PEG3350, PEG4000, PEG5000MME. Protein Buffer: 10 mM Tris pH 8.0, 20 mM NaCl. Drop size: 200 nl protein + 100 nl reservoir.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 67167 / % possible obs: 100 % / Redundancy: 12.95 % / Biso Wilson estimate: 18.25 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.077 / Net I/σ(I): 17.81
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 11.91 % / Mean I/σ(I) obs: 1.95 / Num. unique obs: 4910 / CC1/2: 0.757 / Rrim(I) all: 1.338 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSVERSION Jan 26, 2018 BUILT=20180307data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180307data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→45.38 Å / SU ML: 0.1577 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.741
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1787 3289 4.9 %
Rwork0.155 63794 -
obs0.1562 67083 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.65 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 18 569 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01222969
X-RAY DIFFRACTIONf_angle_d1.18984046
X-RAY DIFFRACTIONf_chiral_restr0.0904473
X-RAY DIFFRACTIONf_plane_restr0.0081517
X-RAY DIFFRACTIONf_dihedral_angle_d11.87241137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.35621440.28842723X-RAY DIFFRACTION99.79
1.47-1.490.26271500.25942737X-RAY DIFFRACTION100
1.49-1.520.26831170.23612740X-RAY DIFFRACTION99.97
1.52-1.550.26211280.22412756X-RAY DIFFRACTION100
1.55-1.570.24881340.21412751X-RAY DIFFRACTION100
1.57-1.60.2111450.20482739X-RAY DIFFRACTION100
1.6-1.640.22221490.19042741X-RAY DIFFRACTION99.97
1.64-1.670.23071350.18692727X-RAY DIFFRACTION100
1.67-1.710.17131500.16952762X-RAY DIFFRACTION99.97
1.71-1.750.18921380.1592753X-RAY DIFFRACTION100
1.75-1.80.18421480.15672747X-RAY DIFFRACTION100
1.8-1.850.19081340.15462746X-RAY DIFFRACTION99.97
1.85-1.910.17431440.15852754X-RAY DIFFRACTION99.97
1.91-1.980.19751480.16062764X-RAY DIFFRACTION99.97
1.98-2.060.15241640.14092741X-RAY DIFFRACTION100
2.06-2.160.17321430.13622778X-RAY DIFFRACTION100
2.16-2.270.16551430.14112782X-RAY DIFFRACTION100
2.27-2.410.1891480.14072767X-RAY DIFFRACTION100
2.41-2.60.17221370.14112804X-RAY DIFFRACTION100
2.6-2.860.16471480.14482793X-RAY DIFFRACTION99.97
2.86-3.270.1591360.14872844X-RAY DIFFRACTION100
3.27-4.120.17291610.13042847X-RAY DIFFRACTION99.87
4.12-45.380.16311450.16452998X-RAY DIFFRACTION99.78
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)
11.154706228940.3852594420430.5689597754331.62821109854-0.2956735792171.75427210366-0.07412673740950.07216781050360.113017598605-0.1972007025050.0100740340440.149472473552-0.054326003516-0.04944586816650.008787519709210.1403786690140.00833502568455-0.01605994401740.14610017821-0.001839040949550.147233744367-16.411176674127.8699840217-25.5144180538
20.328502150958-0.05418683324240.02376724581411.38649085729-0.7288950164820.862068263752-0.0103649529490.00210773512739-0.00625045810389-0.0337746135714-0.0332107283888-0.09346988697680.07160821009560.06548751208040.05492526816040.09626408117980.00747020606203-0.009891262799530.130297881409-0.004890153839460.12052313697-6.736554931034.323664701660.704532847343
30.1694570285660.251997278106-0.002494122598721.635794344450.8788789353760.249228445587-0.02045154393410.0321798982747-0.0735375525490.0407190618792-0.00040245249212-0.0834478246122-0.0377112609739-0.00369531091090.01439109145430.1884795667950.0143296321524-0.03041101255390.1812297546950.006944787768220.184274298075-7.44627837517-31.9341752163-9.75009247541
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 36 through 157 )36 - 1571 - 122
22chain 'A' and (resid 158 through 304 )158 - 304123 - 269
33chain 'A' and (resid 305 through 391 )305 - 391270 - 356

+
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