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- PDB-1qfg: E. COLI FERRIC HYDROXAMATE RECEPTOR (FHUA) -

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Basic information

Entry
Database: PDB / ID: 1qfg
TitleE. COLI FERRIC HYDROXAMATE RECEPTOR (FHUA)
ComponentsPROTEIN (FERRIC HYDROXAMATE UPTAKE RECEPTOR)
KeywordsMETAL TRANSPORT / TONB-DEPENDENT RECEPTOR / INTEGRAL OUTER MEMBRANE PROTEIN / FERRICHROME-IRON RECEPTOR / ACTIVE TRANSPORT / IRON TRANSPORT PROTEIN / LIPOPOLYSACCHARIDE
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
LAURIC ACID / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / DIPHOSPHATE / 3-HYDROXY-TETRADECANOIC ACID / MYRISTIC ACID / NICKEL (II) ION / PHOSPHATE ION / Ferrichrome outer membrane transporter/phage receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFerguson, A.D. / Welte, W. / Hofmann, E. / Lindner, B. / Holst, O. / Coulton, J.W. / Diederichs, K.
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: Non-polymer description / Version format compliance
Revision 1.3Jun 20, 2012Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 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 1.6Jun 24, 2020Group: Data collection / Derived calculations / Category: chem_comp / 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 / 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_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_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.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.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
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

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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)85,03024
Polymers80,0511
Non-polymers4,97923
Water4,396244
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: 80051.109 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH LIPOPOLYSACCHARIDE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Cell: BACTERIAL / Variant: RA CHEMOTYPE / Plasmid: PHX405 / Cellular location (production host): OUTER MEMBRANE / Production host: Escherichia coli (E. coli) / Strain (production host): AW740 / Variant (production host): RA CHEMOTYPE / 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, 266 molecules

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


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: 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
#6: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


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


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H27NO
#9: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 4.65 Å3/Da / Density % sol: 73.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 100MM SODIUM CACODYLATE (PH 6.4), 12.5% PEG 2000 MONOMETHYLETHER, 20% GLYCEROL, 1% CIS-INOSITOL, 3% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
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: MAX II / Beamline: I711 / Wavelength: 1.051
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.051 Å / Relative weight: 1
ReflectionResolution: 2.45→42.3 Å / Num. obs: 53749 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 43.12 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.334 / % possible all: 92.2
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
SOLVEphasing
CNS1refinement
XDSdata scaling
RefinementResolution: 2.5→42.3 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MOD. ENGH&HUBER PROTEIN_REP.PARAM (CNS)
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2309 4.6 %RANDOM
Rwork0.221 ---
obs0.221 50668 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.33 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 65.4 Å2
Baniso -1Baniso -2Baniso -3
1--13.78 Å22.99 Å20 Å2
2---13.78 Å20 Å2
3---27.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5524 0 309 244 6077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.026
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_deg2.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.442
X-RAY DIFFRACTIONc_mcangle_it6.63
X-RAY DIFFRACTIONc_scbond_it7.883
X-RAY DIFFRACTIONc_scangle_it9.264
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 454 5.4 %
Rwork0.412 7897 -
obs--99.2 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.72

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