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- PDB-1h6t: Internalin B: crystal structure of fused N-terminal domains. -

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Basic information

Entry
Database: PDB / ID: 1h6t
TitleInternalin B: crystal structure of fused N-terminal domains.
ComponentsINTERNALIN B
KeywordsCELL ADHESION / LEUCINE RICH REPEAT / IG-LIKE DOMAIN / EF-HAND DOMAIN
Function / homology
Function and homology information


peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / 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 / 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 / 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 / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchubert, W.-D. / Gobel, G. / Diepholz, M. / Darji, A. / Kloer, D. / Hain, T. / Chakraborty, T. / Wehland, J. / Domann, E. / Heinz, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Internalins from the human pathogen Listeria monocytogenes combine three distinct folds into a contiguous internalin domain.
Authors: Schubert, W.D. / Gobel, G. / Diepholz, M. / Darji, A. / Kloer, D. / Hain, T. / Chakraborty, T. / Wehland, J. / Domann, E. / Heinz, D.W.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Internalins from the Human Pathogen Listeria Monocytogenes Combine Three Distinct Folds Into a Contiguous Internalin Domain
Authors: Schubert, W.-D. / Gobel, G. / Diepholz, M. / Darji, A. / Kloer, D. / Hain, T. / Chakraborty, T. / Wehland, J. / Domann, E. / Heinz, D.W.
History
DepositionJun 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _diffrn_source.pdbx_synchrotron_y_n / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERNALIN B


Theoretical massNumber of molelcules
Total (without water)32,3961
Polymers32,3961
Non-polymers00
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.953, 72.818, 115.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INTERNALIN B


Mass: 32395.943 Da / Num. of mol.: 1 / Fragment: LRR DOMAIN, RESIDUES 36-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD (SEROVAR 1/2A) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25147, UniProt: P0DQD2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIVE N-TERMINAL RESIDUES (GLY PRO LEU GLY SER)WERE INTRODUCED AS PART OF THE CLONING STRATEGY ...THE FIVE N-TERMINAL RESIDUES (GLY PRO LEU GLY SER)WERE INTRODUCED AS PART OF THE CLONING STRATEGY (PRESCISSION PROTEASE CLEAVAGE SEQUENCE).

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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: 2.17 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / pH: 5
Details: 0.2M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 5.0, 13% W/V PEG 4000, 6% V/V 2-METHYL-2,4-PENTANDIOL, T=20C, PROTEIN CONC.=10 MG/ML
Crystal grow
*PLUS
Method: sparse matrix method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %(w/v)PEG400011
25 %(v/v)MPD11
30.1 Msodium acetate11
40.22 Mammonium acetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU AFC-5 / Wavelength: 1.5418
DetectorType: RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 10, 2000 / Details: OSMIC CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→61 Å / Num. obs: 37671 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 22
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 7.42 / % possible all: 91.2
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 67222 / % possible obs: 93.2 %
Reflection shell
*PLUS
% possible obs: 88.1 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D0B

1d0b


Resolution: 1.6→62 Å / SU B: 2.22 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1730 5 %RANDOM
Rwork0.165 ---
obs-37124 95.3 %-
Refinement stepCycle: LAST / Resolution: 1.6→62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 0 475 2758
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182 / Rfactor Rfree: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS

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