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- PDB-7pv8: InlB392_T332E: T332E variant of Listeria monocytogenes InlB (inte... -

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Basic information

Entry
Database: PDB / ID: 7pv8
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
Listeria-Bacteroides repeat domain / 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 ...Listeria-Bacteroides repeat domain / 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 / Alpha-Beta Horseshoe / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGeerds, C. / Niemann, H.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionOct 1, 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)40,5513
Polymers40,4501
Non-polymers1012
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint3 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.580, 54.590, 226.720
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 with five N-terminal residues (GPLGS) remaining after human rhinovirus C3 protease (PreScission) cleavage of the GST-tag
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 3.53 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Reservoir solution (Morpheus screen (Molecular Dimensions) condition G2): 0.1 M (imidazole / MES), pH 6.5; 20 % v/v ethylene glycol; 10 % w/v PEG 8,000; 0.02 M sodium formate; 0.02 M ...Details: Reservoir solution (Morpheus screen (Molecular Dimensions) condition G2): 0.1 M (imidazole / MES), pH 6.5; 20 % v/v ethylene glycol; 10 % w/v PEG 8,000; 0.02 M sodium formate; 0.02 M ammonium acetate; 0.02 M sodium citrate tribasic dehydrate; 0.02 M sodium potassium tartrate tetrahydrate; 0.02 M sodium oxamate; 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: 2.05→50 Å / Num. obs: 35861 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 43.1 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.122 / Net I/σ(I): 16.56
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.74 / Num. unique obs: 2598 / CC1/2: 0.792 / Rrim(I) all: 1.956 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSVERSION Jun 1, 2017 BUILT=20170923data reduction
XSCALEVERSION Jun 1, 2017 BUILT=20170923data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H6T, 2Y5P

1h6t

2y5p


Resolution: 2.05→16.15 Å / SU ML: 0.2423 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 1754 4.92 %
Rwork0.1864 33908 -
obs0.1885 35662 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.72 Å2
Refinement stepCycle: LAST / Resolution: 2.05→16.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 5 276 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082895
X-RAY DIFFRACTIONf_angle_d0.82943934
X-RAY DIFFRACTIONf_chiral_restr0.0527461
X-RAY DIFFRACTIONf_plane_restr0.0055504
X-RAY DIFFRACTIONf_dihedral_angle_d13.43331083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.36651440.30032533X-RAY DIFFRACTION99.85
2.11-2.170.35591350.28352542X-RAY DIFFRACTION99.66
2.17-2.240.32851350.26892564X-RAY DIFFRACTION99.67
2.24-2.320.26651200.23882569X-RAY DIFFRACTION99.85
2.32-2.410.27231380.22212569X-RAY DIFFRACTION99.89
2.41-2.520.24521330.21082599X-RAY DIFFRACTION99.89
2.52-2.650.23441350.19532582X-RAY DIFFRACTION99.96
2.65-2.820.23191220.21032624X-RAY DIFFRACTION99.96
2.82-3.030.22881290.20832612X-RAY DIFFRACTION99.96
3.03-3.330.28231290.20822609X-RAY DIFFRACTION99.78
3.33-3.810.26811350.18022639X-RAY DIFFRACTION100
3.81-4.780.16621410.13892672X-RAY DIFFRACTION100
4.78-16.150.17171580.14952794X-RAY DIFFRACTION99.8
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)
11.340652155530.428795332067-1.190437893632.01627368667-1.845575605185.38063204811-0.0124568516224-0.05531853263760.008510903597170.10224971743-0.049154516615-0.175364160226-0.1540954956910.2842067344790.05984492711910.3874316740220.0167140943063-0.03288374083360.3573051297140.01527814629150.3574392106239.4118122451.70644455896-16.2664865453
21.25636195527-1.014201655410.8879881213792.39463505731-2.263884432332.749399451330.202508324214-0.118024643812-0.367884900543-0.2993546029010.09808231125220.4382171515560.326319342946-0.0869314534341-0.3384210869080.408142876598-0.0357598026752-0.05346582867620.3076769189260.0035876141570.35000955903310.3713170641-27.34314149683.53488043972
31.915152242181.176957468072.46530168991.83570897342.733756264656.66371105801-0.07600627600330.204245646895-0.120052518863-0.1634924572540.118347802718-0.09971712606940.1696800717660.24148035283-0.03860644391760.4779874554450.03890824623750.07651807299340.424808829564-0.01564890397190.3946715564534.5556319064-7.69567723729-52.3316170211
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 193 through 304 )193 - 304158 - 269
22chain 'A' and (resid 305 through 392 )305 - 392270 - 357
33chain 'A' and (resid 36 through 192 )36 - 1921 - 157

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