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- PDB-2y5q: Listeria monocytogenes InlB (internalin B) residues 36-392 -

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Basic information

Entry
Database: PDB / ID: 2y5q
TitleListeria monocytogenes InlB (internalin B) residues 36-392
ComponentsINTERNALIN B
KeywordsPROTEIN BINDING / LEUCINE RICH REPEAT / VIRULENCE FACTOR / PATHOGENICITY FACTOR
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 / Leucine-rich repeat, SDS22-like subfamily / 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 / Internalin B
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsEbbes, M. / Niemann, H.H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Fold and Function of the Inlb B-Repeat.
Authors: Ebbes, M. / Bleymuller, W.M. / Cernescu, M. / Nolker, R. / Brutschy, B. / Niemann, H.H.
History
DepositionJan 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / 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 / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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

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Assembly

Deposited unit
A: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6184
Polymers40,4221
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: INTERNALIN B
hetero molecules

A: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2368
Polymers80,8442
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2550 Å2
ΔGint-200.2 kcal/mol
Surface area26720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.400, 126.400, 107.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein INTERNALIN B / INLB


Mass: 40421.789 Da / Num. of mol.: 1 / Fragment: INTERNALIN DOMAIN AND B-REPEAT, RESIDUES 36-392
Source method: isolated from a genetically manipulated source
Details: THE B-REPEAT (RESIDUES 322-392) IS NOT VISIBLE IN THE ELECTRON DENSITY.
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS / References: UniProt: P25147, UniProt: P0DQD2*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Nonpolymer detailsZN ION (ZN): ZN IONS PROBABLY CARRIED OVER FROM ZN CONTAINING SEED SOLUTION. METAL ION VERIFIED BY ...ZN ION (ZN): ZN IONS PROBABLY CARRIED OVER FROM ZN CONTAINING SEED SOLUTION. METAL ION VERIFIED BY ANOMALOUS DIFFERENCE DENSITY.
Sequence detailsFIVE N-TERMINAL RESIDUES GPLGS REMAIN AFTER PRESCISSION PROTEASE CLEAVAGE OF THE GST TAG.

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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: 6.16 Å3/Da / Density % sol: 80 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20 DEG C IN HANGING OR SITTING-DROPS WITH 1.5 UL PROTEIN (5 MG/ML) PLUS 1.5 UL RESERVOIR (0.1 M MES, PH 5.5, 14 % MPD) MICROSEEDED FROM A SIMILAR CONDITION (0.1 M MES PH 6.0, 6.5 % PEG6000 AND 5 MM ZNCL2).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→15 Å / Num. obs: 16581 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 18.3
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6T

1h6t


Resolution: 3.2→14.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 27.176 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22475 829 5 %RANDOM
Rwork0.19713 ---
obs0.19847 15752 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.16 Å2
Baniso -1Baniso -2Baniso -3
1-4.69 Å22.35 Å20 Å2
2--4.69 Å20 Å2
3----7.04 Å2
Refinement stepCycle: LAST / Resolution: 3.2→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 3 0 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222307
X-RAY DIFFRACTIONr_bond_other_d0.0050.021535
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9853131
X-RAY DIFFRACTIONr_angle_other_deg1.13433827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9555288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.27326.9799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.93415437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.471154
X-RAY DIFFRACTIONr_chiral_restr0.10.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
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_it0.6311.51444
X-RAY DIFFRACTIONr_mcbond_other0.1011.5577
X-RAY DIFFRACTIONr_mcangle_it1.24222358
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9733863
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5144.5773
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: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 58 -
Rwork0.296 1105 -
obs--100 %
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)
115.7093-6.72160.2044.9933.78817.16270.284-0.85380.56120.77480.9477-1.0431.48460.9749-1.23170.7498-0.11-0.14440.5167-0.08720.732480.7375-30.623629.2733
25.3310.7004-2.62831.3523-0.24814.0450.1502-0.13970.3124-0.044-0.0551-0.1073-0.14140.1846-0.09510.03510.0131-0.01440.0242-0.02310.072557.6838-35.807337.0795
34.68553.3631-1.39144.7289-1.24942.45020.203-0.5002-0.36360.597-0.18710.04190.2604-0.4135-0.01580.2261-0.1056-0.02340.4003-0.06730.266428.5862-48.930747.9399
45.63093.4922-1.157713.9003-3.58223.36720.1921-0.6695-0.5259-0.1709-0.1780.08890.5668-0.5476-0.01410.2232-0.1343-0.10190.4439-0.04440.27525.3145-52.847645.6577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 45
2X-RAY DIFFRACTION2A46 - 227
3X-RAY DIFFRACTION3A228 - 275
4X-RAY DIFFRACTION4A276 - 321

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