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- PDB-4cu4: FhuA from E. coli in complex with the lasso peptide microcin J25 ... -

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Basic information

Entry
Database: PDB / ID: 4cu4
TitleFhuA from E. coli in complex with the lasso peptide microcin J25 (MccJ25)
Components
  • FERRICHROME-IRON RECEPTOR
  • MICROCIN J25
KeywordsTRANSPORT PROTEIN/ANTIBIOTIC / TRANSPORT PROTEIN-ANTIBIOTIC COMPLEX / LIPOPOLYSACCHARIDE / DETERGENT
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 / killing of cells of another organism / intracellular iron ion homeostasis ...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 / killing of cells of another organism / intracellular iron ion homeostasis / defense response to bacterium / iron ion binding / protein domain specific binding / extracellular region / 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
Microcin J25 / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / LAURIC ACID / DIPHOSPHATE / 3-HYDROXY-TETRADECANOIC ACID / MYRISTIC ACID / PHOSPHATE ION / Ferrichrome outer membrane transporter/phage receptor / Microcin J25
Similarity search - Component
Biological speciesESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria)
ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMathavan, I. / Rebuffat, S. / Beis, K.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Structural Basis for Hijacking Siderophore Receptors by Antimicrobial Lasso Peptides.
Authors: Mathavan, I. / Zirah, S. / Mehmood, S. / Choudhury, H.G. / Goulard, C. / Li, Y. / Robinson, C.V. / Rebuffat, S. / Beis, K.
History
DepositionMar 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Jun 13, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.4Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.5Jul 1, 2020Group: Data collection / Other / Category: chem_comp / pdbx_database_status
Item: _chem_comp.type / _pdbx_database_status.status_code_sf
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.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 20, 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 / 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 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRICHROME-IRON RECEPTOR
B: MICROCIN J25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,62934
Polymers80,2272
Non-polymers8,40232
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint73.9 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.980, 277.050, 106.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein FERRICHROME-IRON RECEPTOR / FHUA / FERRIC HYDROXAMATE RECEPTOR / FERRIC HYDROXAMATE UPTAKE


Mass: 78100.961 Da / Num. of mol.: 1 / Fragment: RESIDUES 53-747
Source method: isolated from a genetically manipulated source
Details: HIS-TAG BETWEEN RESIDUE P405 AND V417. SEQUENCE INSERTED SSHHHHHHGSS
Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria)
Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P06971
#2: Protein/peptide MICROCIN J25 / MICROCIN MCCJ25 / MCCJ25


Type: Polypeptide / Class: Inhibitor / Mass: 2126.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
References: UniProt: Q9X2V7, Microcin J25
#3: Polysaccharide L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy- ...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-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1165.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LDmanHep1-3LDmanHep1-5[DKdopa2-4]DKdopa2-6DGlcpNb1-6DGlcpNa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1a_1-5_2*N][a2122h-1b_1-5_2*N][Aad1122h-2a_2-6][a11221h-1a_1-5]/1-2-3-3-4-4/a6-b1_b6-c2_c4-d2_c5-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpN]{[(6+1)][b-D-GlcpN]{[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}[(5+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 8 types, 199 molecules

#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-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#8: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77O8P
#9: Chemical ChemComp-DPO / DIPHOSPHATE


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsINTRODUCED AN INTERNAL HIS-TAG AFTER POSITION P405 AND V417

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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: 4.44 Å3/Da / Density % sol: 72.3 % / Description: NONE
Crystal growpH: 5
Details: 20 MM TRIS PH 7.5, 120 MM LITHIUM SULFATE, 100 MM SODIUM CITRATE PH 5, 20 % PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2012 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→30.46 Å / Num. obs: 62620 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FCP

2fcp


Resolution: 2.3→30.46 Å / Cor.coef. Fo:Fc: 0.8875 / Cor.coef. Fo:Fc free: 0.8605 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.196 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.186
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. THE ELECTRON DENSITY AT THE INTERNAL HIS-TAG LOOP REGION WAS TOO WEAK TO ALLOW BUILDING RESIDUES 405-417 RELIABLY
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3172 5.07 %RANDOM
Rwork0.212 ---
obs0.2141 62613 98.55 %-
Displacement parametersBiso mean: 56.71 Å2
Baniso -1Baniso -2Baniso -3
1--27.7597 Å20 Å20 Å2
2--27.6669 Å20 Å2
3---0.0927 Å2
Refine analyzeLuzzati coordinate error obs: 0.348 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 512 168 6242
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016221HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.138336HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2888SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes853HARMONIC5
X-RAY DIFFRACTIONt_it6221HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion2.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion751SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6655SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3281 228 4.96 %
Rwork0.2738 4365 -
all0.2764 4593 -
obs--98.55 %

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