[English] 日本語
Yorodumi
- PDB-4we2: Donor strand complemented FaeG of F4ab fimbriae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4we2
TitleDonor strand complemented FaeG of F4ab fimbriae
ComponentsK88 fimbrial protein AB
KeywordsSTRUCTURAL PROTEIN / Adhesin / Lectin / Immunoglobulin-like fold
Function / homologypilus / K88 fimbrial protein AB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMoonens, K. / Van den Broeck, I. / De Kerpel, M. / Deboeck, F. / Raymaekers, H. / Remaut, H. / De Greve, H.
Funding support Belgium, 2items
OrganizationGrant numberCountry
FWOG030411N Belgium
FWO - HerculesUABR/09/005 Belgium
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Functional Insight into the Carbohydrate Receptor Binding of F4 Fimbriae-producing Enterotoxigenic Escherichia coli.
Authors: Moonens, K. / Van den Broeck, I. / De Kerpel, M. / Deboeck, F. / Raymaekers, H. / Remaut, H. / De Greve, H.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K88 fimbrial protein AB


Theoretical massNumber of molelcules
Total (without water)29,1341
Polymers29,1341
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.639, 49.026, 54.468
Angle α, β, γ (deg.)90.00, 109.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein K88 fimbrial protein AB / K88 antigen / K88 pilin


Mass: 29134.211 Da / Num. of mol.: 1 / Fragment: UNP residues 40-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: faeG / Plasmid: pDEST14 / Details (production host): Gateway technology / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: P02970
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18 mM Na/K-phosphate, 18% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→51.43 Å / Num. obs: 41977 / % possible obs: 97.9 % / Redundancy: 3.1 % / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.8 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLR

3hlr


Resolution: 1.5→51.43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.774 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21396 2113 5 %RANDOM
Rwork0.1751 ---
obs0.17704 39847 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.167 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2---0.75 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.5→51.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 0 289 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021983
X-RAY DIFFRACTIONr_bond_other_d0.0010.021865
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.9472700
X-RAY DIFFRACTIONr_angle_other_deg0.9734280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29925.18581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16315311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.486158
X-RAY DIFFRACTIONr_chiral_restr0.130.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
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_it1.2691.2351060
X-RAY DIFFRACTIONr_mcbond_other1.2691.2341059
X-RAY DIFFRACTIONr_mcangle_it1.7891.8541329
X-RAY DIFFRACTIONr_mcangle_other1.7881.8551330
X-RAY DIFFRACTIONr_scbond_it2.2011.495923
X-RAY DIFFRACTIONr_scbond_other2.21.496924
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1962.1511371
X-RAY DIFFRACTIONr_long_range_B_refined6.45412.3642306
X-RAY DIFFRACTIONr_long_range_B_other6.37311.0492145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 126 -
Rwork0.26 2369 -
obs--79.18 %
Refinement TLS params.Method: refined / Origin x: 0.8153 Å / Origin y: -11.3537 Å / Origin z: 16.5151 Å
111213212223313233
T0.0058 Å2-0.0053 Å20.0059 Å2-0.0237 Å2-0.0192 Å2--0.017 Å2
L1.6867 °2-0.3634 °20.6393 °2-1.3929 °2-0.933 °2--2.4291 °2
S0.0359 Å °0.075 Å °-0.0674 Å °-0.0771 Å °0.0201 Å °-0.0563 Å °0.0454 Å °0.0992 Å °-0.056 Å °

+
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