[English] 日本語
Yorodumi
- PDB-3jwn: Complex of FimC, FimF, FimG and FimH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jwn
TitleComplex of FimC, FimF, FimG and FimH
Components
  • Chaperone protein fimC
  • FimH protein
  • Protein fimF
  • Protein fimG
Keywordsprotein binding/cell adhesion / fimbria / cell adhesion / fimh / fimc / fimf / fimg / chaperone / fibrium / immunoglobulin domain / Fimbrium / Periplasm / Disulfide bond / protein binding-cell adhesion COMPLEX
Function / homology
Function and homology information


pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space ...pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / : / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion / metal ion binding
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
FimH protein / Protein FimF / Protein FimG / Chaperone protein FimC / FimH protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLe Trong, I. / Aprikian, P. / Stenkamp, R.E. / Sokurenko, E.V.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting.
Authors: Le Trong, I. / Aprikian, P. / Kidd, B.A. / Forero-Shelton, M. / Tchesnokova, V. / Rajagopal, P. / Rodriguez, V. / Interlandi, G. / Klevit, R. / Vogel, V. / Stenkamp, R.E. / Sokurenko, E.V. / Thomas, W.E.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Chaperone protein fimC
E: Protein fimF
F: Protein fimF
G: Protein fimG
H: FimH protein
I: Chaperone protein fimC
K: Protein fimF
L: Protein fimF
M: Protein fimG
N: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,17212
Polymers197,98710
Non-polymers1842
Water50428
1
C: Chaperone protein fimC
E: Protein fimF
F: Protein fimF
G: Protein fimG
H: FimH protein


Theoretical massNumber of molelcules
Total (without water)98,9945
Polymers98,9945
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-42 kcal/mol
Surface area42520 Å2
MethodPISA
2
I: Chaperone protein fimC
K: Protein fimF
L: Protein fimF
M: Protein fimG
N: FimH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1787
Polymers98,9945
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-43.8 kcal/mol
Surface area42070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.025, 216.025, 532.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
Protein , 4 types, 10 molecules CIEFKLGMHN

#1: Protein Chaperone protein fimC


Mass: 22754.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4316, fimC, JW4279 / Plasmid: PET22B based PTIPKB91 / Production host: Escherichia coli (E. coli) / References: UniProt: P31697
#2: Protein
Protein fimF


Mass: 16161.095 Da / Num. of mol.: 4 / Fragment: UNP residues 23-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4318, fimF, JW4281 / Production host: Escherichia coli (E. coli) / References: UniProt: P08189
#3: Protein Protein fimG


Mass: 14864.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4319, fimG, JW4282 / Production host: Escherichia coli (E. coli) / References: UniProt: P08190
#4: Protein FimH protein


Mass: 29053.260 Da / Num. of mol.: 2 / Fragment: UNP residues 25-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: F18 / Gene: ECP_4655, fimh / Production host: Escherichia coli (E. coli) / References: UniProt: Q0T8Y8, UniProt: A0A0R4I961*PLUS

-
Non-polymers , 2 types, 30 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.03 Å3/Da / Density % sol: 79.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 1.6 M potassium chloride, 0.1 M sodium citrate, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2008
RadiationMonochromator: double-crystal, SI(111), liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→176.8 Å / Num. obs: 119926 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 14
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.862 / % possible all: 46.7

-
Processing

Software
NameVersionClassification
PHASERphasing
MOLREPphasing
REFMAC5.5.0096refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1KLF, 3BWU and 3BFQ

1klf

3bwu

3bfq


Resolution: 2.69→48.34 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.362 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27208 6018 5 %RANDOM
Rwork0.24364 ---
obs0.24506 113836 90.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.028 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13822 0 12 28 13862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214146
X-RAY DIFFRACTIONr_bond_other_d0.0020.028904
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.95319357
X-RAY DIFFRACTIONr_angle_other_deg0.744321955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43651851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92825.262572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.372152120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2311557
X-RAY DIFFRACTIONr_chiral_restr0.0530.22337
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022646
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_it0.3571.59257
X-RAY DIFFRACTIONr_mcbond_other0.0281.53756
X-RAY DIFFRACTIONr_mcangle_it0.658214994
X-RAY DIFFRACTIONr_scbond_it0.50734889
X-RAY DIFFRACTIONr_scangle_it0.8864.54361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 225 -
Rwork0.405 4023 -
obs--43.68 %

+
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