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- PDB-1by5: FHUA FROM E. COLI, WITH ITS LIGAND FERRICHROME -

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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, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / 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 (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / 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 (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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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