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- PDB-1kmo: Crystal structure of the Outer Membrane Transporter FecA -

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Basic information

Entry
Database: PDB / ID: 1kmo
TitleCrystal structure of the Outer Membrane Transporter FecA
ComponentsIron(III) dicitrate transport protein fecA
KeywordsMEMBRANE PROTEIN / Iron transporter / TonB-dependent receptor / Siderophore
Function / homology
Function and homology information


response to iron ion starvation / siderophore-iron transmembrane transporter activity / siderophore-dependent iron import into cell / signal transduction involved in regulation of gene expression / transmembrane transporter complex / cell outer membrane / signaling receptor activity / iron ion transport / 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, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, 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, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / 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
HEPTANE-1,2,3-TRIOL / Fe(3+) dicitrate transport protein FecA
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFerguson, A.D. / Chakraborty, R. / Smith, B.S. / Esser, L. / van der Helm, D. / Deisenhofer, J.
CitationJournal: Science / Year: 2002
Title: Structural basis of gating by the outer membrane transporter FecA.
Authors: Ferguson, A.D. / Chakraborty, R. / Smith, B.S. / Esser, L. / van der Helm, D. / Deisenhofer, J.
History
DepositionDec 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,60220
Polymers85,4061
Non-polymers4,19619
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.083, 88.086, 94.578
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 which is contained within the asymmetric unit

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Components

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


Mass: 85406.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ferric citrate uptake receptor / Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: k-12 / Gene: fecA / Plasmid: pSV66 / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: P13036
#2: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.85 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1000, MOPS, LDAO, heptane-1,2,3-triol, sodium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal grow
*PLUS
Details: Smith, B.S., (1998) Acta Cryst., D54, 697., Doublie, S., (1997) Methods Enzymol., 276, 532.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2000
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 56331 / Num. obs: 56331 / % possible obs: 92.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.13 Å / % possible all: 0.71
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 62452 / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SnBphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 223348.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2830 5 %RANDOM
Rwork0.207 ---
all0.207 56331 --
obs0.207 56331 84.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2134 Å2 / ksol: 0.365878 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.47 Å20 Å20 Å2
2---3.57 Å20 Å2
3----0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 292 386 5862
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 397 5.1 %
Rwork0.28 7400 -
obs-7400 71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5LDAO.PARAMLDAO.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.28

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