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- PDB-1esz: STRUCTURE OF THE PERIPLASMIC FERRIC SIDEROPHORE BINDING PROTEIN F... -

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Basic information

Entry
Database: PDB / ID: 1esz
TitleSTRUCTURE OF THE PERIPLASMIC FERRIC SIDEROPHORE BINDING PROTEIN FHUD COMPLEXED WITH COPROGEN
ComponentsFERRICHROME-BINDING PERIPLASMIC PROTEIN
KeywordsMETAL TRANSPORT / FhuD / iron transport / siderophore binding protein / periplasmic ligand binding protein / ABC transport protein
Function / homology
Function and homology information


ferric-hydroxamate import into cell / iron ion import across plasma membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPROGEN / Iron(3+)-hydroxamate-binding protein FhuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsClarke, T.E. / Braun, V. / Winkelmann, G. / Tari, L.W. / Vogel, H.J.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: X-ray crystallographic structures of the Escherichia coli periplasmic protein FhuD bound to hydroxamate-type siderophores and the antibiotic albomycin.
Authors: Clarke, T.E. / Braun, V. / Winkelmann, G. / Tari, L.W. / Vogel, H.J.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The Structure of the Ferric Siderophore Binding Protein Fhud Complexed with Gallichrome
Authors: Clarke, T.E. / Ku, S.-Y. / Dougan, D. / Vogel, H.J. / Tari, L.W.
History
DepositionApr 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: FERRICHROME-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5162
Polymers29,6941
Non-polymers8221
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.09, 86.09, 91.94
Angle α, β, γ (deg.)90, 90, 120
Int Tables number173
Space group name H-MP63

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Components

#1: Protein FERRICHROME-BINDING PERIPLASMIC PROTEIN


Mass: 29694.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: P07822
#2: Chemical ChemComp-CPO / COPROGEN


Mass: 821.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H53FeN6O13
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na/K phosphate, HEPES, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.3 mg/mlprotein1drop
20.8 Mdisodium/potassium phosphate1drop
30.05 MHEPES1droppH7.5
41.6 Mdisodium/potassium phosphate1reservoir
50.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9787
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 26445 / Num. obs: 25292 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 90.1 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.1
Reflection shellResolution: 2→30 Å / Redundancy: 90.1 % / Rmerge(I) obs: 0.102 / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 90.1 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 6.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2→30 Å / σ(F): 1 / σ(I): 2
Details: Average B factors as reported by the author- Ligand: 31.90 Waters: 35.76
RfactorNum. reflection% reflectionSelection details
Rfree0.241 22625 -random
Rwork0.219 ---
all0.219 26445 --
obs-25292 95.6 %-
Displacement parametersBiso mean: 28.7 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 54 125 2200
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection Rfree: 1165 / Rfactor obs: 0.219 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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