[English] 日本語
Yorodumi
- PDB-3ohn: Crystal structure of the FimD translocation domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ohn
TitleCrystal structure of the FimD translocation domain
ComponentsOuter membrane usher protein FimD
KeywordsMEMBRANE PROTEIN / beta-barrel / protein translocation / outer membrane
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / membrane => GO:0016020 / cell outer membrane
Similarity search - Function
Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain
Similarity search - Domain/homology
Outer membrane usher protein FimD / Outer membrane usher protein FimD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.011 Å
AuthorsWang, T. / Li, H.
CitationJournal: Nature / Year: 2011
Title: Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.
Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. ...Authors: Phan, G. / Remaut, H. / Wang, T. / Allen, W.J. / Pirker, K.F. / Lebedev, A. / Henderson, N.S. / Geibel, S. / Volkan, E. / Yan, J. / Kunze, M.B. / Pinkner, J.S. / Ford, B. / Kay, C.W. / Li, H. / Hultgren, S.J. / Thanassi, D.G. / Waksman, G.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane usher protein FimD
B: Outer membrane usher protein FimD


Theoretical massNumber of molelcules
Total (without water)123,0752
Polymers123,0752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Outer membrane usher protein FimD

B: Outer membrane usher protein FimD


Theoretical massNumber of molelcules
Total (without water)123,0752
Polymers123,0752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
Buried area1630 Å2
ΔGint-17 kcal/mol
Surface area45750 Å2
MethodPISA
3
A: Outer membrane usher protein FimD

B: Outer membrane usher protein FimD


Theoretical massNumber of molelcules
Total (without water)123,0752
Polymers123,0752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.022, 87.132, 95.883
Angle α, β, γ (deg.)63.92, 88.43, 76.94
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Outer membrane usher protein FimD


Mass: 61537.316 Da / Num. of mol.: 2 / Fragment: TRANSLOCATION DOMAIN (unp residues 169-708)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD / Plasmid: pNH297 / Production host: Escherichia coli (E. coli) / Strain (production host): B tuner / References: UniProt: C8U0R5, UniProt: P30130*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Trisodium citrate,pH4.8~6.5, 7% (w/v) PEG4000, 100mM sodium chloride, 50mM Magnesium, 20mM spermine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 27375 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.5 / % possible all: 96

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERPHENIXphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2vqi

2vqi


Resolution: 3.011→28.89 Å / SU ML: 0.44 / σ(F): 1.97 / Phase error: 33.22 / Stereochemistry target values: ML
Details: AUTHORS HAVE APPROVED THIS ENTRY WITH REPORTED R VALUE AS 0.23 WHILE CALCULATED R VALUE IS 0.31. THE DEPOSITED COORDINATES WERE FURTHER MODIFIED IN COOT AFTER FINAL ROUND OF PHENIX REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.3053 1368 5 %random
Rwork0.2295 ---
obs0.2334 27375 98.04 %-
all-27410 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.835 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 61.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.2886 Å24.2899 Å2-5.1891 Å2
2--18.7583 Å2-5.878 Å2
3----10.4697 Å2
Refinement stepCycle: LAST / Resolution: 3.011→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7246 0 0 0 7246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097426
X-RAY DIFFRACTIONf_angle_d1.38710068
X-RAY DIFFRACTIONf_dihedral_angle_d18.112603
X-RAY DIFFRACTIONf_chiral_restr0.091061
X-RAY DIFFRACTIONf_plane_restr0.0051323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0113-3.11880.37841280.26992526X-RAY DIFFRACTION94
3.1188-3.24350.35841250.24272607X-RAY DIFFRACTION99
3.2435-3.39090.30011230.22692601X-RAY DIFFRACTION98
3.3909-3.56930.27851300.20832645X-RAY DIFFRACTION99
3.5693-3.79250.28031560.20212612X-RAY DIFFRACTION99
3.7925-4.08460.29411190.20792631X-RAY DIFFRACTION99
4.0846-4.49430.24641460.18972609X-RAY DIFFRACTION99
4.4943-5.14140.25891250.18782627X-RAY DIFFRACTION99
5.1414-6.46570.33071580.25752599X-RAY DIFFRACTION98
6.4657-28.89160.331580.26712550X-RAY DIFFRACTION97

+
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