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- PDB-1po3: Crystal structure of ferric citrate transporter FecA in complex w... -

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Basic information

Entry
Database: PDB / ID: 1po3
TitleCrystal structure of ferric citrate transporter FecA in complex with ferric citrate
ComponentsIron(III) dicitrate transport protein fecA precursor
KeywordsMEMBRANE PROTEIN / outer membrane protein / beta barrel / TonB-dependent transport / citrate / siderophore / iron
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 receptor, conserved site ...: / 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 receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / 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: 3.4 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: Iron(III) dicitrate transport protein fecA precursor
B: Iron(III) dicitrate transport protein fecA precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,31810
Polymers166,3392
Non-polymers9808
Water00
1
A: Iron(III) dicitrate transport protein fecA precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6595
Polymers83,1691
Non-polymers4904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron(III) dicitrate transport protein fecA precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6595
Polymers83,1691
Non-polymers4904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.489, 147.003, 96.131
Angle α, β, γ (deg.)90.00, 110.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer although asymmetric unit is an NCS-related dimer

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Components

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


Mass: 83169.328 Da / Num. of mol.: 2 / Fragment: FecA residues 95-741
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.: 4 / Fragment: diferric dicitrate / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe

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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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG1000, LDAO, calcium chloride, Bis-Tris, pH 7.5, 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
114 %(w/w)PEG10001reservoir
2100 mM1reservoirCaCl2
30.025 MBis-Tris1reservoirpH7.0
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: NSLS / Beamline: X9B / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2002
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→19.77 Å / Num. all: 33661 / Num. obs: 30446 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 78.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.9
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3036 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 30794 / % possible obs: 100 % / Num. measured all: 135112
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 3036 / Num. measured obs: 13363 / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB accession code 1KMP

1kmp


Resolution: 3.4→15 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: In chain A side chains were not built for residues GLN221, MET249, ARG336, GLN351, ARG385, MET396, TYR499, ASP503, GLU533, ARG582, THR600, GLU616, ASP622, TYR624, LYS668, GLN695 and LYS740. ...Details: In chain A side chains were not built for residues GLN221, MET249, ARG336, GLN351, ARG385, MET396, TYR499, ASP503, GLU533, ARG582, THR600, GLU616, ASP622, TYR624, LYS668, GLN695 and LYS740. In chain B side chains were not built for residues ARG217, ASP222, MET249, HIS295, GLU307, PHE346, GLN351, ARG385, MET396, GLN428, TYR436, LYS454, MET466, GLU485, GLU533, ASP548, TYR592, LYS620 and MET696.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1525 5.1 %RANDOM
Rwork0.239 ---
all0.283 30263 --
obs0.239 30068 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.268617 e/Å3
Displacement parametersBiso mean: 57.4 Å2
Baniso -1Baniso -2Baniso -3
1-15.2 Å20 Å212.44 Å2
2--13.25 Å20 Å2
3----28.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9968 0 56 0 10024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d1.18
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 271 5.4 %
Rwork0.298 4741 -
obs-4741 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CITRATE.PARAMCITRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 3.4 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18

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