[English] 日本語
Yorodumi
- PDB-3f85: Structure of fusion complex of homo trimeric major pilin subunits... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f85
TitleStructure of fusion complex of homo trimeric major pilin subunits CfaB of CFA/I fimbirae from ETEC E. coli
Componentshomo trimeric fusion of CFA/I fimbrial subunits B
KeywordsCELL ADHESION / ETEC / CfaBBB / major pilin / pilus / pili / fimbriae / CFA/I / Cell projection / Fimbrium
Function / homologyCFA/I fimbrial subunit E, pilin domain / Fimbrial major subunit, CS1-type / CS1 type fimbrial major subunit / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / CFA/I fimbrial subunit B / CFA/I fimbrial subunit B
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXia, D. / Li, Y.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli.
Authors: Li, Y.F. / Poole, S. / Nishio, K. / Jang, K. / Rasulova, F. / McVeigh, A. / Savarino, S.J. / Xia, D. / Bullitt, E.
History
DepositionNov 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: homo trimeric fusion of CFA/I fimbrial subunits B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0885
Polymers47,9911
Non-polymers974
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.406, 44.982, 97.880
Angle α, β, γ (deg.)90.00, 125.35, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein homo trimeric fusion of CFA/I fimbrial subunits B / CFA/I pilin / Colonization factor antigen I subunit B / CFA/I antigen


Mass: 47990.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02971, UniProt: E3PPC4*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growMethod: vapor diffusion / pH: 3.5
Details: the CfaBBB protein (10 mg/ml in 20 mM Tri-HCl, pH 7.5, 100 mM NaCl) is crystallized by mixing in 1:1 ratio with 22% PEG 4000, 100 mM ammonium sulfate, 100 mM sodium citrate at pH 3.5, 1% ...Details: the CfaBBB protein (10 mg/ml in 20 mM Tri-HCl, pH 7.5, 100 mM NaCl) is crystallized by mixing in 1:1 ratio with 22% PEG 4000, 100 mM ammonium sulfate, 100 mM sodium citrate at pH 3.5, 1% ethylene glycol, 2% PEG 400, 1% iso-propanol, 10 mM MgCl2, 0.3% 1,2,3 heptanetriol; VAPOR DIFFUSION

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 25005
Reflection shellHighest resolution: 2.1 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.201 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28301 1243 5 %RANDOM
Rwork0.233 ---
obs0.23578 23716 93.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.294 Å2
Baniso -1Baniso -2Baniso -3
1--6.99 Å20 Å2-3.45 Å2
2--4.27 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 4 108 3400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9664538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59327.059102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01115523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.056153
X-RAY DIFFRACTIONr_chiral_restr0.1150.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022405
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1450.21188
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2670.22177
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0150.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1911.52343
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86423678
X-RAY DIFFRACTIONr_scbond_it3.05431126
X-RAY DIFFRACTIONr_scangle_it4.2574.5860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 59 -
Rwork0.309 1275 -
obs--68.48 %
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)
16.81942.08991.24762.66950.15172.88820.04480.11060.1385-0.07920.01890.3350.1683-0.2826-0.0637-0.06620.05160.0493-0.22640.0348-0.2036-21.9421-17.4567-20.9264
24.93331.13633.68651.73260.60425.1297-0.18210.19720.2717-0.17270.05650.3047-0.4001-0.06310.1257-0.1090.00780.0579-0.2711-0.0226-0.167419.8942-0.5996-0.6089
310.19310.62342.71991.57870.05733.56570.276-1.5775-1.61690.2599-0.0325-0.22840.4853-0.0441-0.24340.0758-0.0451-0.04360.21560.26640.104759.9755-5.432329.9842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1511 - 151
2X-RAY DIFFRACTION2AA152 - 302152 - 302
3X-RAY DIFFRACTION3AA303 - 454303 - 454

+
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