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- PDB-1po0: Crystal structure of ferric citrate transporter FecA in complex w... -

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Basic information

Entry
Database: PDB / ID: 1po0
TitleCrystal structure of ferric citrate transporter FecA in complex with iron-free citrate
ComponentsIron(III) dicitrate transport protein fecA precursor
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta barrel / TonB-dependent transport / citrate / siderophore
Function / homology
Function and homology information


response to iron ion starvation / siderophore-iron transmembrane transporter activity / siderophore-iron import into cell / transmembrane transporter complex / signal transduction involved in regulation of gene expression / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / regulation of DNA-templated transcription / membrane
Similarity search - Function
: / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / 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 ...: / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / 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
CITRATE ANION / Fe(3+) dicitrate transport protein FecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsYue, W.W. / Grizot, S. / Buchanan, S.K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural evidence for iron-free citrate and ferric citrate binding to the TonB-dependent outer membrane transporter FecA
Authors: Yue, W.W. / Grizot, S. / Buchanan, S.K.
History
DepositionJun 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: Iron(III) dicitrate transport protein fecA precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5483
Polymers83,1691
Non-polymers3782
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.070, 89.310, 95.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: Protein Iron(III) dicitrate transport protein fecA precursor


Mass: 83169.328 Da / Num. of mol.: 1 / Fragment: FecA residues 81-741
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FECA OR B4291 / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P13036
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Fragment: iron-free dicitrate / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Fragment: water / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG1000, LDAO, sodium citrate, sodium chloride , pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111 %(w/w)PEG10001reservoir
2350 mM1reservoirNaCl
30.025 Msodium citrate1reservoirpH5.5
415 mg/mlprotein1drop
525 mMTris-HCl1droppH8.0
60.1 %LDAO1drop
7350 mM1dropNaCl
83 %(v/v)1,2,3-heptanetriol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2001
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.15→29.06 Å / Num. all: 54025 / Num. obs: 52397 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.5
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3498 / % possible all: 90.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 54094 / % possible obs: 98 % / Num. measured all: 215425
Reflection shell
*PLUS
% possible obs: 90.1 % / Num. unique obs: 3498 / Num. measured obs: 7930 / Rmerge(I) obs: 0.412

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB accession code 1KMO

1kmo


Resolution: 2.15→19.93 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Side chains were not built for residues ASP255, GLU293, GLN428, GLN695 and MET696
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2608 5 %RANDOM
Rwork0.233 ---
all0.246 52350 --
obs0.233 51234 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0399 Å2 / ksol: 0.342783 e/Å3
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.15→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 26 256 5448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.652
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 409 5.1 %
Rwork0.409 7648 -
obs-7648 91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CITRATE.PARAMCITRATE.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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