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- PDB-7nms: InlB392_T332E: T332E variant of Listeria monocytogenes InlB (inte... -

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Basic information

Entry
Database: PDB / ID: 7nms
TitleInlB392_T332E: T332E 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
DI(HYDROXYETHYL)ETHER / Internalin B
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGeerds, C. / Niemann, H.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A recurring packing contact in crystals of InlB pinpoints functional binding sites in the internalin domain and the B repeat.
Authors: Geerds, C. / Bleymuller, W.M. / Meyer, T. / Widmann, C. / Niemann, H.H.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Internalin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0287
Polymers40,4501
Non-polymers5786
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-24 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.410, 88.730, 102.020
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

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Components

#1: Protein Internalin B / InlB / Invasion protein InlB


Mass: 40449.801 Da / Num. of mol.: 1 / Mutation: T332E
Source method: isolated from a genetically manipulated source
Details: residue 36 to 392 of InlB
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: inlB, lmo0434 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P0DQD2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 % / Description: rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Reservoir solution: 0.1 M succinate, pH 7.0, 0.2 M Li2SO4, 22.5 % PEG mixture consisting of equal amounts of eight low molecular weight PEGs (PEG 300, PEG 400, PEG 500MME, PEG 550MME, PEG ...Details: Reservoir solution: 0.1 M succinate, pH 7.0, 0.2 M Li2SO4, 22.5 % PEG mixture consisting of equal amounts of eight low molecular weight PEGs (PEG 300, PEG 400, PEG 500MME, PEG 550MME, PEG 600, PEG 750MME, PEG 1,000, PEG 1,000MME); Protein solution: 10 mg/ml in 10 mM Tris, pH 8.0, 20 mM NaCl; Drop size: 100 nl + 100 nl (protein + reservoir)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 37383 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 1 / Rrim(I) all: 0.069 / Net I/σ(I): 23.59
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.88 / Num. unique obs: 2714 / CC1/2: 0.807 / Rrim(I) all: 159.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
XDSVERSION Jan 26, 2018 BUILT=20180307data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180307data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1h6t, 2y5p

1h6t

2y5p


Resolution: 1.8→26.77 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 1871 5.03 %
Rwork0.1713 35359 -
obs0.1736 37230 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 34 329 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372942
X-RAY DIFFRACTIONf_angle_d0.6474002
X-RAY DIFFRACTIONf_chiral_restr0.0464466
X-RAY DIFFRACTIONf_plane_restr0.0048509
X-RAY DIFFRACTIONf_dihedral_angle_d11.91181100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.35381270.28982683X-RAY DIFFRACTION99.72
1.85-1.90.32351090.2622712X-RAY DIFFRACTION99.89
1.9-1.960.28571530.24192657X-RAY DIFFRACTION99.5
1.96-2.030.24711530.21452665X-RAY DIFFRACTION99.58
2.03-2.120.25931530.19842669X-RAY DIFFRACTION99.58
2.12-2.210.23441520.18372680X-RAY DIFFRACTION99.89
2.21-2.330.22081450.1692712X-RAY DIFFRACTION99.97
2.33-2.470.20741470.16312715X-RAY DIFFRACTION100
2.47-2.670.19241530.16742700X-RAY DIFFRACTION99.89
2.67-2.930.23771380.17742742X-RAY DIFFRACTION99.86
2.93-3.360.20661500.17912760X-RAY DIFFRACTION99.97
3.36-4.230.20251560.1432756X-RAY DIFFRACTION100
4.23-26.770.19661350.15752908X-RAY DIFFRACTION98.77
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)
12.76052956848-0.1149796153071.57544505695.20055304543-1.914895626125.65772999822-0.1429110495280.1583902495630.162337293744-0.3014156495630.09383020579540.207904233226-0.21000516796-0.216523146640.06297913843670.339215773206-0.02712348797460.00147287878840.324325738383-0.04450464942230.326643971935-13.530734837328.1410700576-27.2397786508
21.155131667660.780542103359-0.2576564633093.07141112979-2.139267751663.58097054552-0.04144973806060.05131966624450.01166236122160.127368435117-0.014670917455-0.0933787710644-0.2542322731460.1342465815160.05251824173640.294981144591-0.03149383007080.02204021930660.249971382795-0.02968704826920.28271540008-4.5899622770312.6726816653-5.76482060315
30.472077044572-0.968341680843-0.165707868225.009679212862.004231437881.3326734784-0.0264479517971-0.0714279087038-0.0651424187907-0.01628129246290.01498044296840.0770247286844-0.09078450476870.03026140369390.02670170567280.197505471896-0.02309882545970.03230101971970.2590822395550.00661733970780.237763348426-7.37257861083-12.55750040545.07037090526
45.99480205035-2.99812608106-2.746686737726.133334617821.922594304423.563287812240.04410583309060.535626926319-0.245723608755-0.258561529705-0.2276693238450.164480798661-0.0469224455088-0.2393334214570.1669061498460.237386753837-0.0479964740938-0.05565263859050.358272755666-0.04173409872850.297797100945-5.29234872887-40.1068577103-15.8013645764
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 148 )36 - 1481 - 113
22chain 'A' and (resid 149 through 244 )149 - 244114 - 209
33chain 'A' and (resid 245 through 339 )245 - 339210 - 304
44chain 'A' and (resid 340 through 392 )340 - 392305 - 357

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