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- PDB-5fp1: Crystal structure of the siderophore receptor PiuA from Acinetoba... -

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Basic information

Entry
Database: PDB / ID: 5fp1
TitleCrystal structure of the siderophore receptor PiuA from Acinetobacter baumannii
ComponentsTONB-DEPENDENT SIDEROPHORE RECEPTOR
KeywordsMETAL TRANSPORT / SIDEROPHORE RECEPTOR / OUTER-MEMBRANE PROTEIN
Function / homology
Function and homology information


siderophore uptake transmembrane transporter activity / porin activity / pore complex / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent siderophore receptor / 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
Similarity search - Domain/homology
PHOSPHATE ION / Probable TonB-dependent siderophore receptor PiuA
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMoynie, L. / Tortajada, A. / Naismith, J.H.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structure and Function of the PiuA and PirA Siderophore-Drug Receptors from Pseudomonas aeruginosa and Acinetobacter baumannii.
Authors: Moynie, L. / Luscher, A. / Rolo, D. / Pletzer, D. / Tortajada, A. / Weingart, H. / Braun, Y. / Page, M.G. / Naismith, J.H. / Kohler, T.
History
DepositionNov 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TONB-DEPENDENT SIDEROPHORE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,21210
Polymers78,6661
Non-polymers2,5469
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.120, 100.130, 163.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TONB-DEPENDENT SIDEROPHORE RECEPTOR / IRON TRANSPORT OUTER MEMBRANE RECEPTOR


Mass: 78665.672 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-743
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Plasmid: PTAMAHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: D0CAH3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 4.6
Details: 1 M DIAMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91741
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.94→65.29 Å / Num. obs: 104869 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.6
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FOK

5fok


Resolution: 1.94→65.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.854 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18092 5238 5 %RANDOM
Rwork0.15668 ---
obs0.15789 99548 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.297 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.22 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.94→65.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 104 792 6310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025688
X-RAY DIFFRACTIONr_bond_other_d00.025302
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9527697
X-RAY DIFFRACTIONr_angle_other_deg0.612312248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27225.346260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98215916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7561522
X-RAY DIFFRACTIONr_chiral_restr0.090.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021295
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 377 -
Rwork0.218 7249 -
obs--99.43 %

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