[English] 日本語
Yorodumi
- PDB-4w6x: Co-complex structure of the lectin domain of F18 fimbrial adhesin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w6x
TitleCo-complex structure of the lectin domain of F18 fimbrial adhesin FedF with inhibitory nanobody NbFedF7
Components
  • F18 fimbrial adhesin AC
  • Nanobody NbFedF7
KeywordsCELL ADHESION / Lectin / Fimbriae / Inhibitor
Function / homologyJelly Rolls - #1210 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / F18 fimbrial adhesin AC
Function and homology information
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMoonens, K. / De Kerpel, M. / Coddens, A. / Cox, E. / Pardon, E. / Remaut, H. / De Greve, H.
Funding support Belgium, 2items
OrganizationGrant numberCountry
FWOG030411N Belgium
FWO-HerculesUABR/09/005 Belgium
CitationJournal: Plos One / Year: 2014
Title: Nanobody Mediated Inhibition of Attachment of F18 Fimbriae Expressing Escherichia coli.
Authors: Moonens, K. / De Kerpel, M. / Coddens, A. / Cox, E. / Pardon, E. / Remaut, H. / De Greve, H.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 10, 2024Group: 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F18 fimbrial adhesin AC
B: Nanobody NbFedF7


Theoretical massNumber of molelcules
Total (without water)30,6232
Polymers30,6232
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-4 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.310, 78.610, 108.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein F18 fimbrial adhesin AC / FedF


Mass: 16311.161 Da / Num. of mol.: 1 / Fragment: UNP Residues 35-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fedF / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: Q47212
#2: Antibody Nanobody NbFedF7


Mass: 14311.772 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pDESTR4-R3 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1 M (NH4)2 SO4, 90 mM Na-citrate pH 4.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.88→44.77 Å / Num. obs: 21548 / % possible obs: 97.4 % / Redundancy: 5.7 % / Net I/σ(I): 11.2
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2703 / % possible all: 85.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X1O

2x1o


Resolution: 1.88→63.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.085 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22601 1087 5.1 %RANDOM
Rwork0.18552 ---
obs0.18759 20400 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.457 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å2-0 Å20 Å2
2---0.09 Å20 Å2
3----2.25 Å2
Refinement stepCycle: 1 / Resolution: 1.88→63.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 0 88 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192105
X-RAY DIFFRACTIONr_bond_other_d0.0050.021895
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.9252867
X-RAY DIFFRACTIONr_angle_other_deg0.943.0024365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3645275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49724.15789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49815328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3331510
X-RAY DIFFRACTIONr_chiral_restr0.140.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
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_it1.8831.9621082
X-RAY DIFFRACTIONr_mcbond_other1.881.9611081
X-RAY DIFFRACTIONr_mcangle_it2.7582.931354
X-RAY DIFFRACTIONr_mcangle_other2.7582.9311355
X-RAY DIFFRACTIONr_scbond_it2.8342.2891023
X-RAY DIFFRACTIONr_scbond_other2.8332.2891023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3473.2951511
X-RAY DIFFRACTIONr_long_range_B_refined6.22916.5422270
X-RAY DIFFRACTIONr_long_range_B_other6.22616.4282252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.877→1.926 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 62 -
Rwork0.386 1067 -
obs--71.05 %
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)
13.0142-1.63030.82522.3243-0.44011.6201-0.0710.1466-0.0016-0.05570.0180.07490.02350.0830.0530.0123-0.01330.0010.0226-00.0114-11.2677-9.30189.5149
21.956-0.1354-1.52721.9901-1.09645.77870.0753-0.14090.0840.0506-0.14740.0642-0.10210.06730.07210.02520.0165-0.00380.0674-0.01990.0288-15.1832-16.054737.6951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 147
2X-RAY DIFFRACTION2B1 - 125

+
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