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- PDB-1xkw: Pyochelin outer membrane receptor FptA from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1xkw
TitlePyochelin outer membrane receptor FptA from Pseudomonas aeruginosa
ComponentsFe(III)-pyochelin receptor
KeywordsMEMBRANE PROTEIN / TonB dependent receptor
Function / homology
Function and homology information


: / siderophore uptake transmembrane transporter activity / enterobactin binding / cell outer membrane / signaling receptor activity / membrane => GO:0016020
Similarity search - Function
TonB-dependent receptor-like / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel ...TonB-dependent receptor-like / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / 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
PYOCHELIN FE(III) / Fe(3+)-pyochelin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCobessi, D. / Celia, H. / Pattus, F.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure at high resolution of ferric-pyochelin and its membrane receptor FptA from Pseudomonas aeruginosa
Authors: Cobessi, D. / Celia, H. / Pattus, F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and X-ray diffraction analyses of the outer membrane pyochelin receptor FptA from Pseudomonas aeruginosa
Authors: Cobessi, D. / Celia, H. / Pattus, F.
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe(III)-pyochelin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,22612
Polymers74,2551
Non-polymers1,97211
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.910, 84.540, 162.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fe(III)-pyochelin receptor


Mass: 74254.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: gene fpta / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: CDC5 / References: UniProt: P42512

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Non-polymers , 5 types, 373 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-188 / PYOCHELIN FE(III)


Mass: 378.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14FeN2O3S2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.3 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 4.5 to 9 % PEG 8K or 10 K, 150 mM (NH4)2S04, 25 % ethylene glycol as cryoprotecting agent, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97953 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2→29.3 Å / Num. all: 71021 / Num. obs: 71021 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.065 / Net I/σ(I): 15.45
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.65 / Num. unique all: 4961 / Rsym value: 0.427 / % possible all: 99.1

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XKH

1xkh


Resolution: 2→29.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3230 -RANDOM
Rwork0.222 ---
all-71021 --
obs-71021 99.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5167 0 126 362 5655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.59
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.2753 348 -
Rwork0.2603 --
obs-6959 99.25 %

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