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- PDB-2fcp: FERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 2fcp
TitleFERRIC HYDROXAMATE UPTAKE RECEPTOR (FHUA) FROM E.COLI
ComponentsPROTEIN (FERRIC HYDROXAMATE UPTAKE RECEPTOR)
KeywordsMEMBRANE PROTEIN / TONB-DEPENDENT RECEPTOR / INTEGRAL OUTER MEMBRANE PROTEIN / FERRICHROME-IRON RECEPTOR / ACTIVE TRANSPORT / IRON TRANSPORT PROTEIN
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
ACETOACETIC ACID / AMINOETHANOLPYROPHOSPHATE / 2-TRIDECANOYLOXY-PENTADECANOIC ACID / 3-OXO-PENTADECANOIC ACID / NICKEL (II) ION / Ferrichrome outer membrane transporter/phage receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsHofmann, E. / Ferguson, A.D. / Diederichs, K. / Welte, W.
CitationJournal: 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
DepositionOct 15, 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: Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.pdbx_synonyms / _database_PDB_caveat.text / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_list.comp_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 3.1Aug 19, 2020Group: Data collection
Category: pdbx_entity_branch_descriptor / pdbx_entity_branch_link
Revision 3.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (FERRIC HYDROXAMATE UPTAKE RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3759
Polymers79,8771
Non-polymers3,4988
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.550, 171.550, 87.650
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 PROTEIN (FERRIC HYDROXAMATE UPTAKE RECEPTOR) / FHUA


Mass: 79876.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: OUTER MEMBRANE / Plasmid: PHX405 / Cellular location (production host): OUTER MEMBRANE / Production host: Escherichia coli (E. coli) / Strain (production host): AW740 / References: UniProt: P06971
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-4-O- ...alpha-D-galactopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-4-O-phosphono-D-glycero-beta-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-deoxy-4-O-phosphono-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1891.376 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/7,9,8/[a2122h-1a_1-5_1*OPO/3O/3=O_2*N][a2122h-1a_1-5_2*N_4*OPO/3O/3=O][Aad1122h-2a_2-6][a11221h-1a_1-5][a11222h-1b_1-5_4*OPO/3O/3=O][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3-3-4-5-6-7-7/a6-b1_b6-c2_c4-d2_c5-e1_e3-f1_f3-g1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[][P]{[(0+1)][a-D-GlcpN]{[(6+1)][a-D-GlcpN]{[(4+0)][P]{}[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}[(5+1)][a-D-Manp]{[(3+1)][b-D-Manp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Galp]{}[(6+1)][a-D-Galp]{}}[(4+0)][P]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 106 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-LIL / 2-TRIDECANOYLOXY-PENTADECANOIC ACID


Mass: 454.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H54O4
#5: Chemical ChemComp-AAE / ACETOACETIC ACID / Acetoacetic acid


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3
#6: Chemical ChemComp-LIM / 3-OXO-PENTADECANOIC ACID


Mass: 256.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O3
#7: Chemical ChemComp-EA2 / AMINOETHANOLPYROPHOSPHATE


Mass: 221.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H9NO7P2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 4.66 Å3/Da / Density % sol: 73.61 %
Crystal growpH: 6.4
Details: 100MM NA-CACODYLATE, PH 6.4, 12.5% PEG2000 MME, 20% GLYCEROL, 1% CIS-INOSITOL, 3% PEG200
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16.5 mg/mlprotein1drop
20.1 Msodium cacodylate1reservoirpH6.4
311 %PEG2000MME1reservoir
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: MAX II / Beamline: I711 / Wavelength: 1.051
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / 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: 2.45→30 Å / Num. obs: 53749 / % possible obs: 99.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.3 Å2 / Rsym value: 0.078 / Net I/σ(I): 17
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.334 / % possible all: 92.2
Reflection
*PLUS
Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Lowest resolution: 2.5 Å / % possible obs: 92.2 % / Num. unique obs: 2931 / Rmerge(I) obs: 0.334

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
CNSrefinement
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: OTHER
Starting model: 1FCP

1fcp


Resolution: 2.5→30 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2309 4.6 %RANDOM
Rwork0.242 ---
obs0.242 50668 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 67.4 Å2
Baniso -1Baniso -2Baniso -3
1--13.92 Å22.28 Å20 Å2
2---13.92 Å20 Å2
3---27.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5512 0 222 99 5833
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_deg1.9
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_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.321.5
X-RAY DIFFRACTIONc_mcangle_it9.022
X-RAY DIFFRACTIONc_scbond_it10.042
X-RAY DIFFRACTIONc_scangle_it11.492.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.439 454 5.4 %
Rwork0.421 7897 -
obs--99.2 %
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 DIFFRACTION4FHUA.PARFHUA.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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