[English] 日本語
Yorodumi
- PDB-2y5q: Listeria monocytogenes InlB (internalin B) residues 36-392 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTERNALIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6184
Polymers40,4221
Non-polymers1963
Water0
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

-
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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).

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more