[English] 日本語
Yorodumi
- PDB-7kob: Crystal structure of antigen 43b from Escherichia coli CFT073 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kob
TitleCrystal structure of antigen 43b from Escherichia coli CFT073
ComponentsAntigen 43b
KeywordsMICROBIAL PROTEIN / Autotransporters / Biofilm / Bacterial virulence / Bacterial infection
Function / homology
Function and homology information


cell outer membrane / periplasmic space / cell surface / extracellular region
Similarity search - Function
Adhesin of bacterial autotransporter system / Autochaperone domain type 1 / Adhesin of bacterial autotransporter system, probable stalk / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily ...Adhesin of bacterial autotransporter system / Autochaperone domain type 1 / Adhesin of bacterial autotransporter system, probable stalk / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsMartinez-Ortiz, G.C. / 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: Antigen 43b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9875
Polymers36,6191
Non-polymers3684
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-2 kcal/mol
Surface area14340 Å2
Unit cell
Length a, b, c (Å)32.780, 70.890, 171.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Antigen 43b


Mass: 36618.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: c1273 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2V731
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.4
Details: 100 mM sodium cacodylate pH 6.4, 14% PEG 4000, 20% MPD

-
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: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.08→36.67 Å / Num. obs: 24576 / % possible obs: 98.4 % / Redundancy: 6.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.06 / Rrim(I) all: 0.153 / Net I/σ(I): 8.3 / Num. measured all: 152138 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.08-2.145.90.7631046617690.7270.3270.8332.394.4
9.07-36.675.80.05421633740.9960.0240.05915.398.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.08 Å36.67 Å
Translation2.08 Å36.67 Å

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.5.7data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KH3

4kh3


Resolution: 2.08→36.67 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 1285 5.24 %
Rwork0.1655 23227 -
obs0.1674 24512 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.05 Å2 / Biso mean: 27.2779 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 2.08→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 56 222 2808
Biso mean--70.74 30.62 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072571
X-RAY DIFFRACTIONf_angle_d0.8473480
X-RAY DIFFRACTIONf_dihedral_angle_d14.75387
X-RAY DIFFRACTIONf_chiral_restr0.057408
X-RAY DIFFRACTIONf_plane_restr0.005470
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 (%)
2.08-2.160.26361480.23572412256094
2.16-2.260.2121120.19542443255595
2.26-2.380.23071360.16932517265396
2.38-2.530.221500.17062563271399
2.53-2.730.20971390.175725862725100
2.73-30.19831420.175126162758100
3-3.430.20071530.163626052758100
3.43-4.320.171410.141726752816100
4.32-36.670.19411640.15162810297499
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)
12.99341.10421.47272.22990.77333.13420.1323-0.4751-0.51170.3835-0.1598-0.31150.36120.08160.02470.3526-0.0077-0.01050.20950.09490.2888-31.3073-74.7935233.1672
22.8541.3610.471.99550.43912.5092-0.0382-0.1472-0.13260.2873-0.0536-0.07080.0409-0.00730.03150.18550.00180.0150.13250.01170.1869-34.2573-67.4541226.9718
30.3132-0.0836-0.44711.6533-0.55851.1386-0.00580.0018-0.0404-0.0756-0.0312-0.0430.0366-0.06860.02050.0627-0.0065-0.0150.1338-0.03040.1377-30.2004-51.4145211.082
40.86930.00510.25821.6511-0.57491.1309-0.03450.10730.0351-0.30610.0443-0.093-0.1241-0.0009-0.0330.22250.00820.03530.1469-0.01640.1277-28.8972-28.6681192.5751
51.2517-0.47621.11823.44-0.47221.86160.02020.45030.0014-0.749-0.114-0.09980.04540.1041-0.03060.6089-0.01450.06850.3062-0.01610.1565-30.172-24.1044176.1176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 29 )A0 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 78 )A30 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 226 )A79 - 226
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 325 )A227 - 325
5X-RAY DIFFRACTION5chain 'A' and (resid 326 through 364 )A326 - 364

+
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://pdbjlvh1.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