[English] 日本語
Yorodumi
- PDB-1by5: FHUA FROM E. COLI, WITH ITS LIGAND FERRICHROME -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1by5
TitleFHUA FROM E. COLI, WITH ITS LIGAND FERRICHROME
Components
  • FERRIC HYDROXAMATE UPTAKE PROTEIN
  • FERRICHROME
KeywordsMETAL BINDING PROTEIN / FHUA / MEMBRANE PROTEIN / LIGAND-GATED / IRON TRANSPORT / FERRICHROME
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / virion binding / transmembrane transporter complex / toxic substance binding / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / iron ion binding / protein domain specific binding / membrane
Similarity search - Function
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 receptor, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel ...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 receptor, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / N-OCTYL-2-HYDROXYETHYL SULFOXIDE / Ferrichrome outer membrane transporter/phage receptor / Ferrichrome outer membrane transporter/phage receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Ustilago sphaerogena (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLocher, K.P. / Rees, B. / Koebnik, R. / Mitschler, A. / Moulinier, L. / Rosenbusch, J.P. / Moras, D.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes.
Authors: Locher, K.P. / Rees, B. / Koebnik, R. / Mitschler, A. / Moulinier, L. / Rosenbusch, J.P. / Moras, D.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: Oligomeric States and Siderophore-Binding of the Ligand-Gated Fhua-Protein Forming Channels Across E. Coli Outer Membranes
Authors: Locher, K.P. / Rosenbusch, J.P.
#2: Journal: J.Am.Chem.Soc. / Year: 1980
Title: Crystal Structure of Ferrichrome and a Comparison with the Structure of Ferrichrome A
Authors: Van Der Helm, D. / Baker, J.R. / Eng-Wilmot, D.L. / Hossain, M.B. / Loghry, R.A.
History
DepositionOct 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FERRIC HYDROXAMATE UPTAKE PROTEIN
B: FERRICHROME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,34111
Polymers79,6352
Non-polymers1,7079
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.200, 89.400, 89.900
Angle α, β, γ (deg.)90.00, 95.40, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein FERRIC HYDROXAMATE UPTAKE PROTEIN / FHUA


Mass: 78929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: FHUA_ECOLI, UniProt: P06971*PLUS
#2: Protein/peptide FERRICHROME


Mass: 705.716 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ustilago sphaerogena (fungus)
#3: Chemical
ChemComp-OES / N-OCTYL-2-HYDROXYETHYL SULFOXIDE


Mass: 206.345 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22O2S
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN B IS A CYCLIC PEPTIDE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 63.1 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: protein solution is mixed in a 1:2 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.3 mg/mlprotein1drop
233 %PEG20001reservoir
30.45 M1reservoirNaCl
40.15 M1reservoirNaPi
50.5 %n-octyl-2-hydroxyethyl-sulfoxide1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9998
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.59→30 Å / Num. obs: 30766 / % possible obs: 92.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 61.2 Å2 / Rmerge(I) obs: 0.06
Reflection
*PLUS
Rmerge(I) obs: 0.06

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.4refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1572333.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELYHOOD USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1446 5.1 %RANDOM
Rwork0.184 ---
obs0.184 28508 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å216.86 Å2
2---7.89 Å20 Å2
3---9.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-4.5 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5501 0 105 143 5749
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it3.122
X-RAY DIFFRACTIONc_scangle_it4.52.5
LS refinement shellResolution: 2.6→2.74 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.288 211 5.5 %
Rwork0.259 3654 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMC8E.TOP
X-RAY DIFFRACTION3C8E.PARORN.TOP
X-RAY DIFFRACTION4ORN.PAR
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.259

+
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