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- PDB-3efm: Structure of the alcaligin outer membrane recepteur FauA from Bor... -

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Basic information

Entry
Database: PDB / ID: 3efm
TitleStructure of the alcaligin outer membrane recepteur FauA from Bordetella pertussis
ComponentsFerric alcaligin siderophore receptor
KeywordsMEMBRANE PROTEIN / Membrane receptor / Membrane transporter / Siderophore / Membrane / Receptor / TonB box
Function / homology
Function and homology information


siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity
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
Ferric alcaligin siderophore receptor
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsBrillet, K. / Lauber, E. / Reimmann, C. / Armstrong, S.K. / Cobessi, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Use of an in-house approach to study the three-dimensional structures of various outer membrane proteins: structure of the alcaligin outer membrane transporter FauA from Bordetella pertussis
Authors: Brillet, K. / Meksem, A. / Lauber, E. / Reimmann, C. / Cobessi, D.
History
DepositionSep 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Nov 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Ferric alcaligin siderophore receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8703
Polymers78,6781
Non-polymers1922
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.893, 188.847, 62.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ferric alcaligin siderophore receptor / FauA


Mass: 78677.844 Da / Num. of mol.: 1 / Fragment: UNP residues 36-734
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: fauA, BP2463 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X6A5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.75% C8E4, 0.1M HEPES, pH7.5, 0.3-0.5M NH4SO4, 13-17% MPD, protein concentration 10mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9789 Å
DetectorDetector: FLAT PANEL / Date: May 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.33→29.42 Å / Num. obs: 42320 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.066
Reflection shellResolution: 2.33→2.4 Å / Rsym value: 0.724 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O5P

2o5p


Resolution: 2.33→29.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.176 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25843 2141 5.1 %RANDOM
Rwork0.21892 ---
obs0.22091 40176 100 %-
all-40176 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.904 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---2.96 Å20 Å2
3---1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.33→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 10 136 4530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214482
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9336095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2535565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77623.333213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05415669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg181536
X-RAY DIFFRACTIONr_chiral_restr0.1010.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023476
X-RAY DIFFRACTIONr_nbd_refined0.2120.21716
X-RAY DIFFRACTIONr_nbtor_refined0.30.22952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.25
X-RAY DIFFRACTIONr_mcbond_it0.911.52912
X-RAY DIFFRACTIONr_mcangle_it1.53924509
X-RAY DIFFRACTIONr_scbond_it2.24931813
X-RAY DIFFRACTIONr_scangle_it3.4984.51586
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 144 -
Rwork0.269 2897 -
obs--100 %
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)
10.4525-0.37110.21983.68080.17181.84030.0285-0.0053-0.14570.0349-0.00180.21650.1147-0.2038-0.0267-0.0609-0.0243-0.0066-0.0546-0.0177-0.067932.642727.60821.0831
20.54080.14040.21291.23930.06141.00450.0131-0.0466-0.01670.0411-0.04420.13860.0282-0.16780.031-0.1187-0.02610.0173-0.065-0.0041-0.087330.33429.2175-0.8267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 159
2X-RAY DIFFRACTION2A160 - 652

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