[English] 日本語
Yorodumi
- PDB-4mee: Crystal structure of the transport unit of the autotransporter AI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mee
TitleCrystal structure of the transport unit of the autotransporter AIDA-I from Escherichia coli
ComponentsDiffuse adherence adhesin
KeywordsPROTEIN BINDING / Beta barrel / outer membrane protein / Autotransporter
Function / homology
Function and homology information


: / cell outer membrane / membrane => GO:0016020 / periplasmic space / cell adhesion / cell surface / extracellular region
Similarity search - Function
Adhesin of bacterial autotransporter system / Adhesin of bacterial autotransporter system, probable stalk / Autotransporter beta-domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain ...Adhesin of bacterial autotransporter system / Adhesin of bacterial autotransporter system, probable stalk / Autotransporter beta-domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Outer membrane autotransporter barrel / 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 / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Diffuse adherence adhesin / AIDA-I autotransporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGawarzewski, I. / Tschapek, B. / Hoeppner, A. / Smits, S.H. / Jose, J. / Schmitt, L.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystal structure of the transport unit of the autotransporter adhesin involved in diffuse adherence from Escherichia coli.
Authors: Gawarzewski, I. / DiMaio, F. / Winterer, E. / Tschapek, B. / Smits, S.H. / Jose, J. / Schmitt, L.
History
DepositionAug 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diffuse adherence adhesin


Theoretical massNumber of molelcules
Total (without water)50,9521
Polymers50,9521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.330, 85.850, 134.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Diffuse adherence adhesin


Mass: 50952.492 Da / Num. of mol.: 1 / Fragment: C-terminal domain (unp residues 841-1287)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aidA / Plasmid: pJM007 / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: D7PPP4, UniProt: Q03155*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, and 27.5 % (v/v) PEG 2000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2012
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9173 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.15-3.20.4463.3194.3
3.2-3.30.3144.4194.2
3.3-3.40.2815194.1
3.4-3.50.1996.9193.8
3.5-40.12111.2193.4
4-500.05323190.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
Rosettamodel building
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.67 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.837 / SU B: 47.436 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30639 493 5.1 %RANDOM
Rwork0.24777 ---
obs0.25061 9183 97.85 %-
all-8556 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.524 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å20 Å2
2--3.81 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 3→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 0 0 2234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9113105
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2745299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.08925.755106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.41415333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.06155
X-RAY DIFFRACTIONr_chiral_restr0.0940.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021781
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7974.071208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1626.1021503
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1294.1521079
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.69832287
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded10.03652243
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 33 -
Rwork0.334 679 -
obs--98.61 %
Refinement TLS params.Method: refined / Origin x: -7.7413 Å / Origin y: 5.7019 Å / Origin z: -18.3516 Å
111213212223313233
T0.0327 Å20.0182 Å2-0.0059 Å2-0.1091 Å2-0.0361 Å2--0.0414 Å2
L1.9693 °21.126 °20.6228 °2-2.2289 °21.1627 °2--1.7715 °2
S-0.0705 Å °0.3151 Å °-0.1431 Å °-0.0283 Å °0.158 Å °-0.0853 Å °-0.0117 Å °0.09 Å °-0.0875 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://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