[English] 日本語
Yorodumi
- PDB-1usz: SeMet AfaE-3 adhesin from Escherichia Coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1usz
TitleSeMet AfaE-3 adhesin from Escherichia Coli
ComponentsAFIMBRIAL ADHESIN AFA-III
KeywordsADHESIN / AFAE-3 / AFIMBRIAL ADHESIN / UPEC / DAEC
Function / homology
Function and homology information


Adhesin, Dr-family / Adhesin, Dr family, signal peptide / Dr-family adhesin / Dr family adhesin / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Afimbrial adhesin AFA-III
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.28 Å
AuthorsAnderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Roversi, P. / Simpson, P. / Chen, H.A. / Urvil, P. / Dumerle, L. / Barlow, P. ...Anderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Roversi, P. / Simpson, P. / Chen, H.A. / Urvil, P. / Dumerle, L. / Barlow, P. / Medof, E. / Smith, R.A.G. / Nowicki, B. / Le Bouguenec, C. / Lea, S.M. / Matthews, S.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: High Resolution Studies of the Afa/Dr Adhesin Drae and its Interaction with Chloramphenicol
Authors: Pettigrew, D. / Anderson, K.L. / Billington, J. / Cota, E. / Simpson, P. / Urvil, P. / Rabuzin, F. / Roversi, P. / Nowicki, B. / Du Merle, L. / Le Bouguenec, C. / Matthews, S. / Lea, S.M.
#1: Journal: Mol.Cell / Year: 2004
Title: An Atomic Resolution Model for Assmebly, Architecture,and Function of the Dr Adhesins
Authors: Anderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Simpson, P. / Roversi, P. / Chen, H.A. / Urvil, P. / Du Merle, L. / Barlow, P.N. / Medof, M.E. / Smith, R.A.G. / Nowicki, B. / Le ...Authors: Anderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Simpson, P. / Roversi, P. / Chen, H.A. / Urvil, P. / Du Merle, L. / Barlow, P.N. / Medof, M.E. / Smith, R.A.G. / Nowicki, B. / Le Bouguenec, C. / Lea, S.M. / Matthews, S.
History
DepositionDec 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AFIMBRIAL ADHESIN AFA-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3653
Polymers16,2341
Non-polymers1322
Water724
1
A: AFIMBRIAL ADHESIN AFA-III
hetero molecules

A: AFIMBRIAL ADHESIN AFA-III
hetero molecules

A: AFIMBRIAL ADHESIN AFA-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0969
Polymers48,7013
Non-polymers3956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPQS
Unit cell
Length a, b, c (Å)141.300, 141.300, 141.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
DetailsTHE MONOMER SITS AROUND THE THREEFOLD AXIS AND FORMS ATRIMER WITH ITS THREEFOLD-RELATED COPIES; THE TRIMER ISLINKED INTERNALLY BY INTERMOLECULAR DISULPHIDE BONDS.

-
Components

#1: Protein AFIMBRIAL ADHESIN AFA-III / AFAE3


Mass: 16233.725 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE DERIVATIVE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: A30 / Description: N-TERMINUS 6-HIS-TAGGED / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q57254
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A GLY 21 TO ALA 21 ENGINEERED MUTATION IN CHAIN A SER 22 TO GLY 22
Sequence detailsMUTATIONS A0G, G1S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 67 % / Description: SOLVED BY SAD WITH AUTOSHARP
Crystal growpH: 7
Details: 2.0 M AMMONIUM SULPHATE, 2% PEG 400, 0.1M NAHEPES PH 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97892
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.1→28.9 Å / Num. obs: 5108 / % possible obs: 99.7 % / Redundancy: 23 % / Biso Wilson estimate: -2.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.8
Reflection shellResolution: 3.1→3.27 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
XFITmodel building
SCALAdata scaling
RANTANphasing
SHARPphasing
SOLOMONphasing
XFITphasing
TNT5Erefinement
RefinementMethod to determine structure: MAD / Resolution: 3.28→30 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO / Details: MAXIMUM LIKELIHOOD BUSTER-TNT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.247 713 5 %RANDOM
Rwork0.218 ---
all0.22 3941 --
obs0.22 3941 99.7 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 37 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 3.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 6 4 1069
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00610852
X-RAY DIFFRACTIONt_angle_deg0.66714753
X-RAY DIFFRACTIONt_dihedral_angle_d20.716360
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.007302
X-RAY DIFFRACTIONt_gen_planes0.0131575
X-RAY DIFFRACTIONt_it1.268108520
X-RAY DIFFRACTIONt_nbd0.032425
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

+
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