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- PDB-1o6t: Internalin (INLA, Listeria monocytogenes) - functional domain, un... -

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Basic information

Entry
Database: PDB / ID: 1o6t
TitleInternalin (INLA, Listeria monocytogenes) - functional domain, uncomplexed
ComponentsINTERNALIN A
KeywordsCELL INVASION / BACTERIAL INFECTION / LEUCINE RICH REPEAT / CELL ADHESION / CELL-WALL SURFACE PROTEIN
Function / homology
Function and homology information


InlA-mediated entry of Listeria monocytogenes into host cells / peptidoglycan-based cell wall / extracellular region
Similarity search - Function
: / 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 ...: / 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 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 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 A / Internalin A
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchubert, W.-D. / Urbanke, C. / Ziehm, T. / Beier, V. / Machner, M.P. / Domann, E. / Wehland, J. / Chakraborty, T. / Heinz, D.W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure of Internalin, a Major Invasion Protein of Listeria Monocytogenes, in Complex with its Human Receptor E-Cadherin
Authors: Schubert, W.-D. / Urbanke, C. / Ziehm, T. / Beier, V. / Machner, M.P. / Domann, E. / Wehland, J. / Chakraborty, T. / Heinz, D.W.
History
DepositionOct 15, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERNALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,73514
Polymers50,2391
Non-polymers1,49613
Water12,647702
1
A: INTERNALIN A
hetero molecules

A: INTERNALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,47028
Polymers100,4782
Non-polymers2,99126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3110 Å2
ΔGint-1.3 kcal/mol
Surface area46280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.919, 55.881, 97.780
Angle α, β, γ (deg.)90.00, 113.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2213-

HOH

21A-2637-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein INTERNALIN A


Mass: 50239.133 Da / Num. of mol.: 1 / Fragment: FUNCTIONAL DOMAIN, RESIDUES 36-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD-E / Variant: SEROVAR 1/2A / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25146, UniProt: P0DJM0*PLUS

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Non-polymers , 6 types, 715 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFIRST FIVE RESIDUES (GPLGS) INTRODUCED THROUGH CLONING PROCEDURE

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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: 2.42 Å3/Da / Density % sol: 48.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: METHOD: VAPOUR DIFFUSION / HANGING DROP, PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0, RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2. CRYSTALS GREW APPROX 2 ...Details: METHOD: VAPOUR DIFFUSION / HANGING DROP, PROTEIN: 10 MG/ML IN 10 MM HEPES PH 7.0, RESEVOIR: 10% PEG 4000, 100 MM MES/TRIS PH 6.0, 100 MM AMMONIUM SULFATE, 10 MM CACL2. CRYSTALS GREW APPROX 2 YEARS AFTER SETUP. TRUE CRYSTALLIZATION CONDITIONS PROBABLY DEVIATE FROM THOSE INDICATED
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %(w/v)PEG40001reservoir
3100 mMMES-Tris1reservoirpH6.0
4100 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.8→25.1 Å / Num. obs: 50336 / % possible obs: 92 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.4 / % possible all: 84.3
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. obs: 62613 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.63 Å / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→91.29 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.384 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.161 3170 5.1 %RANDOM
Rwork0.131 ---
obs0.133 59440 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-0.37 Å2
2--0.78 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 79 702 4286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0214504
X-RAY DIFFRACTIONr_bond_other_d0.0020.023982
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.9796265
X-RAY DIFFRACTIONr_angle_other_deg0.85739459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1240.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025279
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02743
X-RAY DIFFRACTIONr_nbd_refined0.3150.31070
X-RAY DIFFRACTIONr_nbd_other0.2650.35443
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.52833
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.5889
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.190.56
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.335
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.391
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.593
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.32122855
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14334780
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.97321649
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.20531485
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 222
Rwork0.206 4201
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.141
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.75

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