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- PDB-3qlb: Enantiopyochelin outer membrane TonB-dependent transporter from P... -

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Basic information

Entry
Database: PDB / ID: 3qlb
TitleEnantiopyochelin outer membrane TonB-dependent transporter from Pseudomonas fluorescens bound to the ferri-enantiopyochelin
ComponentsEnantio-pyochelin receptor
KeywordsMETAL TRANSPORT / Membrane protein / Transport / Ferri-enantiopyochelin / Outer membrane
Function / homology
Function and homology information


siderophore uptake transmembrane transporter activity / 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 / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain ...TonB-dependent receptor-like / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / 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
CITRIC ACID / ENANTIO-PYOCHELIN FE(III) / Enantio-pyochelin receptor
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsBrillet, K. / Noel, S. / Mislin, G.L.A. / Reimmann, C. / Schalk, I.J. / Cobessi, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Pyochelin enantiomers and their outer-membrane siderophore transporters in fluorescent pseudomonads: structural bases for unique enantiospecific recognition
Authors: Brillet, K. / Reimmann, C. / Mislin, G.L.A. / Noel, S. / Rognan, D. / Schalk, I.J. / Cobessi, D.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Enantio-pyochelin receptor
B: Enantio-pyochelin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0068
Polymers163,6732
Non-polymers1,3336
Water0
1
A: Enantio-pyochelin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5034
Polymers81,8371
Non-polymers6663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enantio-pyochelin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5034
Polymers81,8371
Non-polymers6663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.070, 170.830, 232.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROVALVALAA23 - 57673 - 626
21PROPROVALVALBB23 - 57673 - 626
12ARGARGTRPTRPAA588 - 698638 - 748
22ARGARGTRPTRPBB588 - 698638 - 748

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Components

#1: Protein Enantio-pyochelin receptor / FetA


Mass: 81836.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: fetA / Plasmid: pME7583 / Production host: Pseudomonas fluorescens (bacteria) / References: UniProt: C5I2D9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EFE / ENANTIO-PYOCHELIN FE(III)


Mass: 378.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14FeN2O3S2
Sequence detailsFIVE HISTIDINE RESIDUES ARE PURIFICATION TAGS.

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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: 4.71 Å3/Da / Density % sol: 73.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 14% PEG1500, 0.1M lithium sulfate, 0.1M sodium citrate, 20% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.95024 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2010 / Details: Mirrors
RadiationMonochromator: double Si [1 1 1] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95024 Å / Relative weight: 1
ReflectionResolution: 3.25→48.57 Å / Num. all: 48366 / Num. obs: 48366 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 78.6 Å2 / Rsym value: 0.137 / Net I/σ(I): 16.11
Reflection shellResolution: 3.26→3.34 Å / Redundancy: 8.1 % / Num. unique all: 3436 / Rsym value: 0.659 / % possible all: 96.4

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Processing

Software
NameVersionClassification
X-NEMOdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BY3

1by3


Resolution: 3.26→48.57 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.89 / SU B: 47.764 / SU ML: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 2426 5 %RANDOM
Rwork0.21419 ---
all0.21648 48332 --
obs0.21648 45793 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.493 Å2
Baniso -1Baniso -2Baniso -3
1-9.99 Å20 Å20 Å2
2---1.69 Å20 Å2
3----8.3 Å2
Refinement stepCycle: LAST / Resolution: 3.26→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10449 0 80 0 10529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210770
X-RAY DIFFRACTIONr_angle_refined_deg2.0791.96514680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68851339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29124.023527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.368151682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3671582
X-RAY DIFFRACTIONr_chiral_restr0.1180.21597
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218406
X-RAY DIFFRACTIONr_mcbond_it0.6411.56664
X-RAY DIFFRACTIONr_mcangle_it1.228210704
X-RAY DIFFRACTIONr_scbond_it1.52534106
X-RAY DIFFRACTIONr_scangle_it2.7414.53976
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2631TIGHT POSITIONAL0.270.05
2495LOOSE POSITIONAL0.565
2631TIGHT THERMAL2.040.5
2495LOOSE THERMAL2.4110
LS refinement shellResolution: 3.255→3.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 151 -
Rwork0.296 3273 -
obs--95.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13430.24540.10151.60490.00340.7831-0.0312-0.0229-0.00050.07860.1364-0.2180.1691-0.1309-0.10520.1929-0.042-0.09540.2320.0290.117848.685-36.1349-5.1081
2-0.0140.2221-0.09451.80480.03461.04080.07550.050.05150.09330.079-0.25140.0772-0.1621-0.15450.05130.0157-0.07460.1554-0.02530.059751.0602-29.3465-7.2741
30.72420.8871-0.64261.45330.04691.380.059-0.05260.0019-0.0269-0.09030.1709-0.03640.05120.03130.1004-0.0073-0.02130.17240.02290.175342.4356-30.529950.1903
40.66660.63510.08380.76970.05951.1945-0.0475-0.01040.1178-0.01690.0920.04280.05040.0371-0.04450.11530.03640.01440.11610.04560.046447.0469-25.054451.9184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 160
2X-RAY DIFFRACTION2A161 - 698
3X-RAY DIFFRACTION3B23 - 160
4X-RAY DIFFRACTION4B161 - 698

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