[English] 日本語
Yorodumi
- PDB-1qjq: FERRIC HYDROXAMATE RECEPTOR FROM ESCHERICHIA COLI (FHUA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qjq
TitleFERRIC HYDROXAMATE RECEPTOR FROM ESCHERICHIA COLI (FHUA)
ComponentsFERRIC HYDROXAMATE RECEPTOR
KeywordsTONB DEPENDENT RECEPTOR / LIPOPOLYSACCHARIDE / FERRICHROME-IRON RECEPTOR / INTEGRAL OUTER MEMBRANE PROTEIN / TONB-DEPENDENT RECEPTOR / SIDEROPHORE RECEPTOR / ACTIVE TRANSPORT / IRON TRANSPORT / SIDEROPHORE-ANTIBIOTIC CONJUGATE
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / virion binding / 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-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DIPHOSPHATE / 3-HYDROXY-TETRADECANOIC ACID / NICKEL (II) ION / PHENYLFERRICROCIN-IRON / PHOSPHATE ION / Ferrichrome outer membrane transporter/phage receptor
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsFerguson, A.D. / Braun, V. / Fiedler, H.-P. / Coulton, J.W. / Diederichs, K. / Welte, W.
Citation
Journal: Protein Sci. / Year: 2000
Title: Crystal structure of the antibiotic albomycin in complex with the outer membrane transporter FhuA.
Authors: Ferguson, A.D. / Braun, V. / Fiedler, H.P. / Coulton, J.W. / Diederichs, K. / Welte, W.
#1: Journal: Protein Sci. / Year: 1998
Title: An Internal Affinity-Tag for Purification and Crystallization of the Siderophore Receptor Fhua, Integral Outer Membrane Protein from Escherichia Coli K-12
Authors: Ferguson, A.D. / Breed, J. / Diederichs, K. / Welte, W. / Coulton, J.W.
#2: Journal: Science / Year: 1998
Title: Siderophore-Mediated Iron Transport: Crystal Structure of Fhua with Bound Lipopolysaccharide
Authors: Ferguson, A.D. / Hofmann, E. / Coulton, J.W. / Diederichs, K. / Welte, W.
History
DepositionJun 29, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_database_status / struct_conn
Item: _chem_comp.type / _citation.page_last ..._chem_comp.type / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 1, 2020Group: Advisory / Data collection / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FERRIC HYDROXAMATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91814
Polymers80,0511
Non-polymers4,86713
Water7,116395
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)172.100, 172.100, 87.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsBIOLOGICAL_UNIT: MONOMER

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein FERRIC HYDROXAMATE RECEPTOR / FHUA


Mass: 80051.109 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: A HEXAHISTIDINE TAG PLUS FIVE ADDITIONAL LINKER RESIDUES HAVE BEEN GENETICALLY INSERTED AFTER RESIDUE 405 OF THE MATURE FHUA SEQUENCE AS AN AFFINITY TAG
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Cell: BACTERIAL / Cellular location: OUTER MEMBRANE / Gene: FHUA / Variant: RA CHEMOTYPE / Plasmid: PHX405 / Cell (production host): BACTERIAL / Cellular location (production host): CYTOPLASM / Gene (production host): FHUA405.H6 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): AW740 / Variant (production host): RA CHEMOTYPE / References: UniProt: P06971
#2: Polysaccharide alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D- ...alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose-(1-6)-2-amino-2,3-dideoxy-alpha-D-glucoyranose


Type: oligosaccharide / Mass: 1973.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/5,11,10/[a2d22h-1a_1-5_2*N][Aad1122h-2a_2-6][a11221h-1a_1-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-1-2-2-3-3-4-4-4-5-3/a6-b1_b6-c2_c4-d2_c5-e1_e3-f1_f3-g1_f7-k1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 1.1.0
[][a-D-3-deoxy-GlcpN]{[(6+1)][b-D-3-deoxy-GlcpN]{[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}[(5+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(2+1)][b-D-Glcp]{}}[(6+1)][a-D-Galp]{}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 6 types, 407 molecules

#3: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O3
#4: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-PFC / PHENYLFERRICROCIN-IRON


Mass: 830.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H48FeN9O12
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsRESIDUES 406 - 416 RESULT FROM A HEXAHISTIDINE TAG PLUS FIVE ADDITIONAL LINKER RESIDUES (P405-SSHHHHHHGSS)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 74 %
Crystal growpH: 6.4
Details: 100MM SODIUM CACODYLATE (PH 6.4), 14.5% PEG 2000 MONOMETHYLETHER, 20% GLYCEROL, 3% PEG 200, 1 MM PHENYLFERRICROCIN-IRON
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Details: equal volume of protein and reservoir solution were used for the drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.80 %N,N-dimethyldecylamine-N-oxide1drop
310 mMammonium acetate1drop
412 %mPEG20001reservoir
50.1 Msodium cacodylate1reservoir
620 %glycerol1reservoir
71 %cis-inositol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.051
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.051 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 32078 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: -0.7 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.062 / Net I/σ(I): 20.26
Reflection shellResolution: 2.95→2.99 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.03 / Rsym value: 0.251 / % possible all: 77.7
Reflection
*PLUS
Num. obs: 31400 / Num. measured all: 231385
Reflection shell
*PLUS
% possible obs: 82 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.8

-
Processing

Software
NameVersionClassification
CNS0.4refinement
XDSdata reduction
XSCALEdata scaling
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFF

1qff


Resolution: 2.95→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1210970.9 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1494 4.9 %RANDOM
Rwork0.225 ---
obs0.225 30289 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.518 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 70.8 Å2
Baniso -1Baniso -2Baniso -3
1--20.14 Å22.89 Å20 Å2
2---20.14 Å20 Å2
3---40.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5523 0 300 395 6218
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.451.5
X-RAY DIFFRACTIONc_mcangle_it3.962
X-RAY DIFFRACTIONc_scbond_it3.632
X-RAY DIFFRACTIONc_scangle_it5.352.5
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 239 4.9 %
Rwork0.326 4635 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

+
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