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- PDB-1qkc: ESCHERICHIA COLI FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) IN COM... -

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Basic information

Entry
Database: PDB / ID: 1qkc
TitleESCHERICHIA COLI FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) IN COMPLEX DELTA TWO-ALBOMYCIN
ComponentsFERRIC HYDROXAMATE RECEPTOR
KeywordsTONB DEPENDENT RECEPTOR / TONB-DEPENDENT RECEPTOR / INTEGRAL OUTER MEMBRANE PROTEIN / FERRICHROME / SIDEROPHORE RECEPTOR / ANTIBIOTIC / ALBOMYCIN / ACTIVE TRANSPORTER / IRON TRANSPORT PROTEIN
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 / protein domain specific binding / iron ion 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
DELTA-2-ALBOMYCIN A1 / DIPHOSPHATE / 3-HYDROXY-TETRADECANOIC ACID / NICKEL (II) ION / PHOSPHATE ION / Ferrichrome outer membrane transporter/phage receptor
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionJul 18, 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 1.4Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _entity_src_gen.pdbx_host_org_cell / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Oct 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 1.6Jul 1, 2020Group: Advisory / Data collection / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_struct_conn_angle / 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_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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRIC HYDROXAMATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,14914
Polymers80,0511
Non-polymers5,09813
Water5,981332
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)171.800, 171.800, 86.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

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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 K-12 / Strain: AW740 / Cell: BACTERIAL / Cellular location: OUTER MEMBRANE / Gene: FHUA / Variant: RA-CHEMOTYPE / Plasmid: PHX405 / Cellular location (production host): CYTOPLASM / Gene (production host): FHUA405.H6 / Production host: Escherichia coli K-12 / 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-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1989.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/6,11,10/[a2122h-1a_1-5_2*N][a2d22h-1a_1-5_2*N][Aad1122h-2a_2-6][a11221h-1a_1-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3-3-4-4-5-5-5-6-4/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-ManpN]{[(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)][a-D-Glcp]{}}[(6+1)][a-D-Galp]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 344 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


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


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


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-ALB / DELTA-2-ALBOMYCIN A1


Mass: 1045.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H57FeN12O18S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 74 %
Crystal growpH: 6.4
Details: 100 MM SODIUM CACODYLATE (PH 6.4), 14.0% POLYETHYLGLYCOL 2000 MONOMETHYLETHER, 20% GLYCEROL, 3% POLYETHYLGLYCOL 200, 1% CIS-INOSITOL, 0.3 MM DELTA TWO ALBOMYCIN
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

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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: 3.1→30 Å / Num. obs: 38021 / % possible obs: 94.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.153 / Rsym value: 0.139 / Net I/σ(I): 6.2
Reflection shellResolution: 3.09→3.2 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.349 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 197612
Reflection shell
*PLUS
% possible obs: 94.3 %

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Processing

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

1qff


Resolution: 3.1→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 136290.09 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1247 5 %RANDOM
Rwork0.222 ---
obs0.222 25029 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.033 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 82.4 Å2
Baniso -1Baniso -2Baniso -3
1--14.98 Å215.27 Å20 Å2
2---14.98 Å20 Å2
3---29.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5523 0 312 332 6167
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
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_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.221.5
X-RAY DIFFRACTIONc_mcangle_it3.52
X-RAY DIFFRACTIONc_scbond_it2.972
X-RAY DIFFRACTIONc_scangle_it4.712.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 216 5.4 %
Rwork0.311 3799 -
obs--91.6 %
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_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.82

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