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- PDB-4cil: YopM-InlB: Hybrid leucine-rich repeat protein -

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Basic information

Entry
Database: PDB / ID: 4cil
TitleYopM-InlB: Hybrid leucine-rich repeat protein
ComponentsYOPM-CAP, INTERNALIN B
KeywordsSIGNALING PROTEIN / CAPPING / FUSION PROTEIN / LRR / PROTEIN CHIMERA / PROTEIN DESIGN / PROTEIN ENGINEERING
Function / homology
Function and homology information


InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / 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-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / 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 / 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
Internalin B / Yop effector YopM
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
LISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBreitsprecher, D. / Niemann, H.H.
CitationJournal: Bmc Struct.Biol. / Year: 2014
Title: Crystal Structure of an Engineered Yopm-Inlb Hybrid Protein.
Authors: Breitsprecher, D. / Gherardi, E. / Bleymuller, W.M. / Niemann, H.H.
History
DepositionDec 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YOPM-CAP, INTERNALIN B


Theoretical massNumber of molelcules
Total (without water)32,1711
Polymers32,1711
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.210, 30.680, 135.390
Angle α, β, γ (deg.)90.00, 90.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2178-

HOH

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Components

#1: Protein YOPM-CAP, INTERNALIN B


Mass: 32170.664 Da / Num. of mol.: 1
Fragment: YOPM N-TERMINAL CAP RESIDUES 34-87, INLB LEUCINE-RICH REPEAT AND INTER-REPEAT REGION RESIDUES 93-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria), (gene. exp.) LISTERIA MONOCYTOGENES (bacteria)
Strain: W22703, EGD-E / Description: PLASMID PYVE227 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS / References: UniProt: P74988, UniProt: P25147
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsONLY RESIDUES 93-321 ARE CONTAINED IN THE FUSION PROTEIN. ONLY RESIDUES 34-87 ARE CONTAINED IN THE ...ONLY RESIDUES 93-321 ARE CONTAINED IN THE FUSION PROTEIN. ONLY RESIDUES 34-87 ARE CONTAINED IN THE FUSION PROTEIN.

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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: 1.91 Å3/Da / Density % sol: 35.6 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: HANGING DROP VAPOUR DIFFUSION AT 293 K WITH A DROP SIZE OF 2 UL CONSISTING OF EQUAL VOLUMES OF PROTEIN AT A CONCENTRATION OF 10 MG/ML AND RESERVOIR SOLUTION (0.1 M TRICINE, PH 9.0, 28% PEG ...Details: HANGING DROP VAPOUR DIFFUSION AT 293 K WITH A DROP SIZE OF 2 UL CONSISTING OF EQUAL VOLUMES OF PROTEIN AT A CONCENTRATION OF 10 MG/ML AND RESERVOIR SOLUTION (0.1 M TRICINE, PH 9.0, 28% PEG 1000, 10% GLYCEROL, 0.25M KCL). CRYSTALS WERE CRYO-PROTECTED WITH RESERVOIR-SOLUTION ADDITIONALLY CONTAINING 15% GLYCEROL AND FLASH-FROZEN IN LIQUID NITROGEN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 38095 / % possible obs: 96.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.88
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.8 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1H6T AND 1JL5

1h6t

1jl5


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.869 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21874 1901 5 %RANDOM
Rwork0.17495 ---
obs0.17712 36193 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.462 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å2-0.82 Å2
2---0.95 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 0 250 2468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192310
X-RAY DIFFRACTIONr_bond_other_d0.0020.021570
X-RAY DIFFRACTIONr_angle_refined_deg2.2181.9853142
X-RAY DIFFRACTIONr_angle_other_deg1.1333887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.66425.943106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63615432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.275159
X-RAY DIFFRACTIONr_chiral_restr0.130.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02410
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 121 -
Rwork0.303 2251 -
obs--85.54 %
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)
14.1595-1.7768-0.14161.8874-0.51444.48430.18250.32540.0277-0.3558-0.0170.22960.2362-0.3776-0.16550.0789-0.026-0.05870.16590.01370.0552-20.9536-2.91955.8014
24.5328-2.64371.40422.6198-0.35183.65030.22140.2677-0.4184-0.1984-0.0280.50120.4589-0.1232-0.19340.1469-0.0156-0.00960.2066-0.01120.1623-18.0871-4.929311.7482
30.6636-0.16340.73380.7117-0.01151.6258-0.01640.0405-0.02360.0431-0.00620.05720.0229-0.03760.02260.0187-0.00160.03040.049-0.00420.0504-8.7814-4.059930.0493
40.4733-0.2367-0.39931.63391.67951.9746-0.033-0.05-0.0104-0.2146-0.0450.1861-0.19-0.01310.0780.05920.0129-0.01630.0480.00190.097-0.335112.727752.5301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 77
2X-RAY DIFFRACTION2A78 - 100
3X-RAY DIFFRACTION3A101 - 230
4X-RAY DIFFRACTION4A231 - 321

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