[English] 日本語
Yorodumi
- PDB-6as8: F9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6as8
TitleF9 pilus adhesin FmlH lectin domain from E. coli UTI89 co-crystallized with ortho-biphenyl-2'-carboxyl N-acetyl-beta-galactosaminoside
ComponentsFml fimbrial adhesin FmlD
KeywordsSUGAR BINDING PROTEIN / Fimbrial adhesin / lectin / bacterial adhesion
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-BTG / Putative Fml fimbrial adhesin FmlD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsKalas, V. / Hultgren, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)108840 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2018
Title: Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection.
Authors: Kalas, V. / Hibbing, M.E. / Maddirala, A.R. / Chugani, R. / Pinkner, J.S. / Mydock-McGrane, L.K. / Conover, M.S. / Janetka, J.W. / Hultgren, S.J.
History
DepositionAug 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fml fimbrial adhesin FmlD
B: Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6754
Polymers35,8402
Non-polymers8352
Water2,270126
1
A: Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3372
Polymers17,9201
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fml fimbrial adhesin FmlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3372
Polymers17,9201
Non-polymers4171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.957, 51.519, 117.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21B-357-

HOH

-
Components

#1: Protein Fml fimbrial adhesin FmlD


Mass: 17920.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: fmlD, UTI89_C1716 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1RBS0
#2: Sugar ChemComp-BTG / ortho-biphenyl-2'-carboxyl N-acetyl-beta-galactosaminoside / 2'-{[2-(acetylamino)-2-deoxy-beta-D-galactopyranosyl]oxy}[1,1'-biphenyl]-3-carboxylic acid


Type: D-saccharide / Mass: 417.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.7 M LiSO4, 2% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16455 / % possible obs: 87.7 % / Redundancy: 10.7 % / Rpim(I) all: 0.041 / Net I/σ(I): 16.08
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 412 / CC1/2: 0.815 / Rpim(I) all: 0.26 / % possible all: 44.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AOW

6aow


Resolution: 2.101→47.183 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.11
RfactorNum. reflection% reflection
Rfree0.2398 824 5.02 %
Rwork0.2008 --
obs0.2028 16419 87.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.101→47.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 60 126 2508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032450
X-RAY DIFFRACTIONf_angle_d0.8113362
X-RAY DIFFRACTIONf_dihedral_angle_d10.847836
X-RAY DIFFRACTIONf_chiral_restr0.029386
X-RAY DIFFRACTIONf_plane_restr0.003426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1009-2.23250.318900.27191597X-RAY DIFFRACTION55
2.2325-2.40490.29531140.23272237X-RAY DIFFRACTION77
2.4049-2.64690.27971350.22862730X-RAY DIFFRACTION93
2.6469-3.02990.25261640.21772943X-RAY DIFFRACTION100
3.0299-3.8170.21961570.18272966X-RAY DIFFRACTION100
3.817-47.19450.21591640.18233122X-RAY DIFFRACTION100

+
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