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- PDB-2grx: Crystal structure of TonB in complex with FhuA, E. coli outer mem... -

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Basic information

Entry
Database: PDB / ID: 2grx
TitleCrystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for ferrichrome
Components
  • Ferrichrome-iron receptor
  • Protein tonB
KeywordsMETAL TRANSPORT / BETA BARREL / OUTER MEMBRANE / HETEROCOMPLEX / INTER-PROTEIN BETA SHEET / PROTEIN-PROTEIN
Function / homology
Function and homology information


Metal ion assimilation from the host / receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / siderophore transmembrane transport / siderophore-iron import into cell / cobalamin transport / intracellular monoatomic cation homeostasis / siderophore transport / siderophore uptake transmembrane transporter activity ...Metal ion assimilation from the host / receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / siderophore transmembrane transport / siderophore-iron import into cell / cobalamin transport / intracellular monoatomic cation homeostasis / siderophore transport / siderophore uptake transmembrane transporter activity / Iron assimilation using enterobactin / plasma membrane protein complex / transmembrane transporter complex / virion binding / cell envelope / Heme assimilation / toxic substance binding / cell outer membrane / transmembrane transport / protein transport / signaling receptor activity / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / iron ion binding / protein domain specific binding / membrane / plasma membrane
Similarity search - Function
TolA/TonB C-terminal domain / TonB / : / TonB polyproline region / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal ...TolA/TonB C-terminal domain / TonB / : / TonB polyproline region / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / DIPHOSPHATE / 2-AMINO-VINYL-PHOSPHATE / FERRICROCIN-IRON / 3-HYDROXY-TETRADECANOIC ACID / MYRISTIC ACID / PHOSPHATE ION / Protein TonB / Ferrichrome outer membrane transporter/phage receptor / Protein TonB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPawelek, P.D. / Allaire, M. / Coulton, J.W.
CitationJournal: Science / Year: 2006
Title: Structure of TonB in complex with FhuA, E. coli outer membrane receptor.
Authors: Pawelek, P.D. / Croteau, N. / Ng-Thow-Hing, C. / Khursigara, C.M. / Moiseeva, N. / Allaire, M. / Coulton, J.W.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / 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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_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.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 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / pdbx_entry_details ...chem_comp_atom / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_stereo_config

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferrichrome-iron receptor
B: Ferrichrome-iron receptor
C: Protein tonB
D: Protein tonB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,87225
Polymers210,0494
Non-polymers6,82321
Water00
1
A: Ferrichrome-iron receptor
C: Protein tonB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,32212
Polymers105,0252
Non-polymers3,29710
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint23 kcal/mol
Surface area32000 Å2
MethodPISA
2
B: Ferrichrome-iron receptor
D: Protein tonB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,55013
Polymers105,0252
Non-polymers3,52611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)234.32, 91.84, 138.51
Angle α, β, γ (deg.)90.000, 118.86, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Ferrichrome-iron receptor / Ferric hydroxamate uptake / Ferric hydroxamate receptor


Mass: 80051.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fhuA / Production host: Escherichia coli (E. coli) / Strain (production host): AW740 / References: UniProt: P06971
#2: Protein Protein tonB


Mass: 24973.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tonB / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P94739, UniProt: P02929*PLUS

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Sugars , 1 types, 2 molecules

#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)] ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]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: 940.849 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[a2d22h-1a_1-5_2*N][Aad1122h-2a_2-6][a11221h-1a_1-5]/1-1-2-2-3/a6-b1_b6-c2_c4-d2_c5-e1WURCSPDB2Glycan 1.1.0
[][D-1,3-deoxy-GlcpN]{[(6+1)][a-D-3-deoxy-GlcpN]{[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}[(5+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 19 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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.: 8 / Source method: obtained synthetically / Formula: C14H28O3
#6: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7P2
#7: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#8: Chemical ChemComp-EAP / 2-AMINO-VINYL-PHOSPHATE


Mass: 139.047 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO4P
#9: Chemical ChemComp-FCI / FERRICROCIN-IRON


Mass: 770.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H44FeN9O13
#10: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% polyethylene glycol 4000, 50 mM MES (pH 6.0), 75 mM NaCl, 5% glycerol, 0.7% C8E4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.932 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 39013 / Num. obs: 38697 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 68.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.7
Reflection shellResolution: 3.3→3.51 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5883 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FCP

1fcp


Resolution: 3.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 2325 6 %FREE R VALUE TEST SET SELECTION: SHELLS
Rwork0.284 ---
all0.297 39013 --
obs0.299 38697 99.2 %-
Solvent computationBsol: 25.447 Å2
Displacement parametersBiso mean: 98.6 Å2
Baniso -1Baniso -2Baniso -3
1-23.31 Å20 Å220.3 Å2
2---17.87 Å20 Å2
3----5.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.49 Å
Luzzati d res low-6 Å
Luzzati sigma a0.59 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12108 0 425 0 12533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.676
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.434 372 -
Rwork0.4 --
obs-5883 97.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2lps_trunc.param
X-RAY DIFFRACTION3fci.param

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