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- PDB-1h6u: Internalin H: crystal structure of fused N-terminal domains. -

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Basic information

Entry
Database: PDB / ID: 1h6u
TitleInternalin H: crystal structure of fused N-terminal domains.
ComponentsINTERNALIN H
KeywordsCELL ADHESION / LEUCINE RICH REPEAT / IG-LIKE DOMAIN / EF-HAND DOMAIN
Function / homology
Function and homology information


cell envelope / extracellular region / membrane
Similarity search - Function
Internalin N-terminal Cap domain-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 / : ...Internalin N-terminal Cap domain-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 / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Helicase, Ruva Protein; domain 3 / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Class 1 internalin InlH
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 25, 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 / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _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

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Assembly

Deposited unit
A: INTERNALIN H


Theoretical massNumber of molelcules
Total (without water)32,5861
Polymers32,5861
Non-polymers00
Water7,260403
1
A: INTERNALIN H

A: INTERNALIN H


Theoretical massNumber of molelcules
Total (without water)65,1712
Polymers65,1712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_456-x-1/2,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)57.481, 100.682, 119.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein INTERNALIN H


Mass: 32585.611 Da / Num. of mol.: 1 / Fragment: LRR DOMAIN, RESIDUES 36-343
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: Q9ZEY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TWO N-TERMINAL RESIDUES (GLY SER) WERE INTRODUCED AS PART OF THE CLONING STRATEGY (PRESCISSION ...THE TWO N-TERMINAL RESIDUES (GLY SER) WERE INTRODUCED AS PART OF THE CLONING STRATEGY (PRESCISSION PROTEASE CLEAVAGE SEQUENCE). RESIDUE 114 IS ALA RATHER THAN THR. THIS HAS BEEN VERIFIED BY SEQUENCING. THE REASON FOR THE DIECREPANCY IS UNKNOWN.

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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: 10% PEG 8000, 0.1M TRIS PH 7.0, 0.2 M MGCL2. T=20C, PROTEIN CONC.=10 MG/ML
Crystal grow
*PLUS
pH: 7 / Method: sparse matrix method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG800011
20.1 MTris11
30.2 M11MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 3, 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
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Num. obs: 32149 / % possible obs: 98.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 96.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D0B

1d0b


Resolution: 1.8→76.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.536 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1652 5.1 %RANDOM
Rwork0.167 ---
obs0.17 30497 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.8→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 0 403 2699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222377
X-RAY DIFFRACTIONr_bond_other_d0.0010.022194
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.9891.9673277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.01835187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1410.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022588
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02359
X-RAY DIFFRACTIONr_nbd_refined0.2250.3489
X-RAY DIFFRACTIONr_nbd_other0.2130.32297
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5315
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7520.533
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3431.51556
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18822578
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5443821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.474.5697
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 107
Rwork0.265 2187
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.21 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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