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- PDB-1qff: E. COLI FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1qff
TitleE. COLI FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) IN COMPLEX WITH BOUND FERRICHROME-IRON
ComponentsFERRIC HYDROXAMATE UPTAKE RECEPTOR
KeywordsMETAL TRANSPORT / TONB-DEPENDENT RECEPTOR / INTEGRAL OUTER MEMBRANE PROTEIN / SIDEROPHORE-IRON RECEPTOR / ACTIVE TRANSPORT / LIPOPOLYSACCHARIDE / FERRICHROME RECEPTOR
Function / homology
Function and homology information


siderophore transmembrane transport / siderophore-iron import into cell / 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 ...siderophore transmembrane transport / siderophore-iron import into cell / 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, plug domain / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / 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 siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / 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
LAURIC ACID / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / DIPHOSPHATE / 2-AMINO-VINYL-PHOSPHATE / FERRICROCIN-IRON / 3-HYDROXY-TETRADECANOIC ACID / MYRISTIC ACID / PHOSPHATE ION / Ferrichrome outer membrane transporter/phage receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsFerguson, A.D. / Hofmann, E. / Coulton, J.W. / Diederichs, K. / Welte, W.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins.
Authors: Ferguson, A.D. / Welte, W. / Hofmann, E. / Lindner, B. / Holst, O. / Coulton, J.W. / Diederichs, K.
#1: 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.
#2: 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.
History
DepositionApr 10, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2012Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jun 27, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.6Nov 27, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation / struct_conn
Item: _chem_comp.type / _citation.page_last ..._chem_comp.type / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
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 / 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_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 2.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRIC HYDROXAMATE UPTAKE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,23815
Polymers80,5201
Non-polymers4,71814
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.400, 171.400, 85.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein FERRIC HYDROXAMATE UPTAKE RECEPTOR / FHUA


Mass: 80520.062 Da / Num. of mol.: 1
Mutation: SER-SER-HIS-HIS-HIS-HIS-HIS-HIS-GLY-SER-SER AFFINITY TAG
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH LIPOPOLYSACCHARIDE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Variant: RA CHEMOTYPE / Plasmid: PHX405 / Cellular location (production host): OUTER MEMBRANE / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 DL41 / References: UniProt: P06971
#2: Polysaccharide alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-L-glycero- ...alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-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: 1635.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/6,9,8/[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]/1-2-3-3-4-4-5-5-6/a6-b1_b6-c2_c4-d2_c5-e1_e3-f1_f3-g1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[][a-D-3-deoxy-GlcpN]{[(6+1)][a-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]{}[(6+1)][a-D-Galp]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 9 types, 165 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O3
#5: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#7: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#8: Chemical ChemComp-EAP / 2-AMINO-VINYL-PHOSPHATE


Mass: 139.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO4P
#9: Chemical ChemComp-FCI / FERRICROCIN-IRON


Mass: 770.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H44FeN9O13
#10: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H27NO
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.6 Å3/Da / Density % sol: 72.75 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.5 mg/mlprotein1drop
20.1 Msodium cacodylate1reservoir
311 %mPEG20001reservoir
420 %glycerol1reservoir
53 %PEG2001reservoir
60.8 %dimethyldecylamine-N-oxide1reservoir
71 %cis-inositol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→46.94 Å / Num. obs: 39663 / % possible obs: 98.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 60.4 Å2 / Rsym value: 0.079
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rsym value: 0.406 / % possible all: 98

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Processing

Software
NameClassification
XSCALEdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 655667.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1676 4.3 %RANDOM
Rwork0.231 ---
obs0.231 38894 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.82 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 64.9 Å2
Baniso -1Baniso -2Baniso -3
1--17.21 Å21.64 Å20 Å2
2---17.21 Å20 Å2
3---34.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5524 0 296 152 5972
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.282
X-RAY DIFFRACTIONc_mcangle_it6.383
X-RAY DIFFRACTIONc_scbond_it6.593
X-RAY DIFFRACTIONc_scangle_it8.864
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 144 2.3 %
Rwork0.319 6190 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4CARBOHYDRATE.PARAM
X-RAY DIFFRACTION5FHUA.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 64.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_mcangle_it3
X-RAY DIFFRACTIONc_scangle_it4
LS refinement shell
*PLUS
Rfactor Rfree: 0.379 / % reflection Rfree: 2.3 % / Rfactor Rwork: 0.319

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