[English] 日本語
Yorodumi
- PDB-6e4v: The Crystal Structure of FhuE from E. coli in complex with its su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e4v
TitleThe Crystal Structure of FhuE from E. coli in complex with its substrate Coprogen
ComponentsFhuE receptor
KeywordsTRANSPORT PROTEIN / TonB-Dependent Transporter / Coprogen / Gram-negative bacteria / outer membrane / Iron Transport
Function / homology
Function and homology information


: / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane => GO:0016020
Similarity search - Function
TonB-dependent receptor-like / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel ...TonB-dependent receptor-like / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
COPROGEN / FhuE receptor
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGrinter, R. / Lithgow, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106077/Z/14/Z United Kingdom
CitationJournal: Iucrj / Year: 2019
Title: Determination of the molecular basis for coprogen import by Gram-negative bacteria.
Authors: Grinter, R. / Lithgow, T.
History
DepositionJul 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine.pdbx_diffrn_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FhuE receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7577
Polymers77,4741
Non-polymers2,2846
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.190, 103.860, 118.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein FhuE receptor / Outer-membrane receptor for Fe(III)-coprogen / Fe(III)-ferrioxamine B and Fe(III)-rhodotrulic acid


Mass: 77473.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: fhuE, b1102, JW1088 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 DE3 / References: UniProt: P16869
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-HWS / COPROGEN / {5-[(hydroxy-kappaO){3-[5-(3-{(hydroxy-kappaO)[5-hydroxy-3-methyl-1-(oxo-kappaO)pent-2-en-1-yl]amino}propyl)-3,6-dioxopiperazin-2-yl]propyl}amino]-3-methyl-5-(oxo-kappaO)pent-3-en-1-yl N~2~-acetyl-N~5~-hydroxy-kappaO-N~5~-[5-hydroxy-3-methyl-1-(oxo-kappaO)pent-2-en-1-yl]-L-ornithinatato(3-)}iron


Mass: 821.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H53FeN6O13
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.75 % / Description: Rectangular rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M PCB 4 pH, 25 %w/v PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2018
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→47.55 Å / Num. obs: 57586 / % possible obs: 99.9 % / Redundancy: 30.5 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.592 / Rpim(I) all: 0.109 / Net I/σ(I): 4.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 26.1 % / Rmerge(I) obs: 3.98 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4121 / Rpim(I) all: 0.813 / % possible all: 99

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EFM

3efm


Resolution: 2→47.57 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.853 / SU R Cruickshank DPI: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.339 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.225
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1741 5.04 %RANDOM
Rwork0.206 ---
obs0.208 34551 60.1 %-
Displacement parametersBiso mean: 42.83 Å2
Baniso -1Baniso -2Baniso -3
1--10.7558 Å20 Å20 Å2
2---9.182 Å20 Å2
3---19.9379 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5319 0 154 196 5669
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095747HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117948HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1952SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes956HARMONIC5
X-RAY DIFFRACTIONt_it5747HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion17.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion726SEMIHARMONIC5
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_contact6118SEMIHARMONIC4
LS refinement shellResolution: 2→2.11 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2512 -4.19 %
Rwork0.1597 663 -
all0.1632 692 -
obs--8.25 %
Refinement TLS params.Method: refined / Origin x: 14.0605 Å / Origin y: 13.0222 Å / Origin z: 26.203 Å
111213212223313233
T-0.202 Å2-0.0066 Å20.0098 Å2--0.1604 Å20.0447 Å2--0.4638 Å2
L1.6367 °2-0.1012 °2-0.0617 °2-1.2356 °20.1222 °2--0.3577 °2
S-0.0507 Å °-0.0084 Å °0.0774 Å °0.182 Å °0.0024 Å °0.0175 Å °0.0388 Å °0.0383 Å °0.0483 Å °
Refinement TLS groupSelection details: { *|* }

+
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