[English] 日本語
Yorodumi
- PDB-7ko9: Crystal structure of antigen 43 from uropathogenic Escherichia co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ko9
TitleCrystal structure of antigen 43 from uropathogenic Escherichia coli UTI89
ComponentsAidA-I family adhesin
KeywordsMICROBIAL PROTEIN / Autotransporters / Biofilm / Bacterial virulence / Bacterial infection
Function / homologyCITRIC ACID / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsVo, J.L. / Hor, L. / Paxman, J.J. / Heras, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)180102987 Australia
Australian Research Council (ARC)150102287 Australia
National Health and Medical Research Council (NHMRC, Australia)1143638 Australia
CitationJournal: NPJ Biofilms Microbiomes / Year: 2022
Title: Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms.
Authors: Vo, J.L. / Ortiz, G.C.M. / Totsika, M. / Lo, A.W. / Hancock, S.J. / Whitten, A.E. / Hor, L. / Peters, K.M. / Ageorges, V. / Caccia, N. / Desvaux, M. / Schembri, M.A. / Paxman, J.J. / Heras, B.
History
DepositionNov 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AidA-I family adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3079
Polymers56,5201
Non-polymers7878
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint11 kcal/mol
Surface area20890 Å2
Unit cell
Length a, b, c (Å)129.280, 132.820, 47.250
Angle α, β, γ (deg.)90.000, 94.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein AidA-I family adhesin / Antigen 43 / Autotransporter adhesin Ag43 / Autotransporter domain-containing protein / Putative ...Antigen 43 / Autotransporter adhesin Ag43 / Autotransporter domain-containing protein / Putative antigen 43 (Fluffing protein)


Mass: 56519.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: flu, AC789_1c11300, CT146_19135, EA231_25565, HmCmsJML146_03717, NCTC9434_03577
Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E1L650

-
Non-polymers , 5 types, 205 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.2
Details: 20% 2-propanol, 100 mM trisodium citrate/citric acid pH 5.2, 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.43→39.42 Å / Num. obs: 28779 / % possible obs: 96.3 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.054 / Rrim(I) all: 0.105 / Net I/σ(I): 9.9 / Num. measured all: 106281 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 % / % possible all: 96.1

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.43-2.520.6971129330080.7440.4160.8132
9.09-39.420.02621465720.9990.0160.0325.4

-
Processing

Software
NameVersionClassification
Aimless0.3.5data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KH3

4kh3


Resolution: 2.43→39.42 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 1325 4.61 %
Rwork0.1646 27434 -
obs0.1666 28759 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.09 Å2 / Biso mean: 50.0801 Å2 / Biso min: 26.88 Å2
Refinement stepCycle: final / Resolution: 2.43→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 52 197 4079
Biso mean--65.04 49.97 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073913
X-RAY DIFFRACTIONf_angle_d0.9275309
X-RAY DIFFRACTIONf_dihedral_angle_d11.035578
X-RAY DIFFRACTIONf_chiral_restr0.06621
X-RAY DIFFRACTIONf_plane_restr0.005714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.530.27081300.25223039316996
2.53-2.640.30881600.23863026318696
2.64-2.780.24971710.21373024319596
2.78-2.960.27431380.19483062320096
2.96-3.180.25041340.1753066320097
3.18-3.50.20281640.16473039320397
3.5-4.010.18451380.1423054319296
4.01-5.050.15111450.12193052319796
5.05-39.420.20351450.16353072321795
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)
14.68920.18651.8420.9930.0773.92550.1512-0.943-0.13220.2385-0.1189-0.04950.31760.4878-0.05890.417-0.00280.02120.84140.04570.2846177.7896-16.5086126.5372
25.27350.45753.25560.90590.99083.2052-0.097-0.13260.06190.0376-0.03380.1418-0.01850.16480.07750.2924-0.05030.01920.26060.00950.2786153.6906-15.1988105.6928
31.59050.85441.03823.17722.19033.433-0.0801-0.00720.1654-0.1237-0.07950.0001-0.1799-0.01310.19390.23470.0021-0.00230.26880.03750.3171135.197-24.885883.3709
42.7354-1.52550.45116.92770.81621.92560.14510.1572-0.317-0.2742-0.0034-0.33320.21880.3209-0.11730.3310.08690.05760.3791-0.02960.3203140.0339-50.403365.9441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 142 )A2 - 142
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 276 )A143 - 276
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 416 )A277 - 416
4X-RAY DIFFRACTION4chain 'A' and (resid 417 through 561 )A417 - 561

+
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