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- PDB-1kmp: Crystal structure of the Outer Membrane Transporter FecA Complexe... -

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Basic information

Entry
Database: PDB / ID: 1kmp
TitleCrystal structure of the Outer Membrane Transporter FecA Complexed with Ferric Citrate
ComponentsIRON(III) DICITRATE TRANSPORT PROTEIN FECA
KeywordsMEMBRANE PROTEIN / Integral outer membrane protein / TonB-dependent receptor / 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
CITRIC ACID / : / Fe(3+) dicitrate transport protein FecA
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 1.3Nov 2, 2011Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Apr 3, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)90,27621
Polymers86,1101
Non-polymers4,16620
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.467, 88.762, 95.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly of this protein is a monomer which is complete within the asymmetric unit

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Components

#1: Protein IRON(III) DICITRATE TRANSPORT PROTEIN FECA / FECA


Mass: 86109.695 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1000, MOPS, sodium chloride, LDAO, heptane-1,2,3-triol, glycerol, 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: APS / Beamline: 19-BM / Wavelength: 1.0003 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2001 / Details: Synchrotron
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 57464 / Num. obs: 57464 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.66 Å / % possible all: 0.723
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 34980

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SnBphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: Phase information was derived from an additional selenomethionyl derivative

Resolution: 2.5→36.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 470835.04 / 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
Rfree0.282 2830 4.9 %RANDOM
Rwork0.242 ---
all0.242 57464 --
obs0.242 57464 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6268 Å2 / ksol: 0.375823 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å20 Å2
2---0.98 Å20 Å2
3----2.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 284 252 5615
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 388 4.9 %
Rwork0.353 7605 -
obs-7605 72.3 %
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 DIFFRACTION5FDC.PARAMFDC.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: 25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.39 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.353

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