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- PDB-1k2v: E. COLI PERIPLASMIC PROTEIN FHUD COMPLEXED WITH DESFERAL -

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Basic information

Entry
Database: PDB / ID: 1k2v
TitleE. COLI PERIPLASMIC PROTEIN FHUD COMPLEXED WITH DESFERAL
ComponentsFerrichrome-binding periplasmic protein
KeywordsMETAL TRANSPORT / two domains / alpha helix linker
Function / homology
Function and homology information


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
DEFEROXAMINE MESYLATE FE(III) COMPLEX / Iron(3+)-hydroxamate-binding protein FhuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsClarke, T.E. / Braun, V. / Winkelmann, G. / Tari, L.W. / Vogel, H.J.
CitationJournal: 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.
History
DepositionSep 29, 2001Deposition 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 1.3Aug 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
N: Ferrichrome-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4162
Polymers29,6941
Non-polymers7221
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.57, 85.57, 91.6
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 / FHUD


Mass: 29694.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fhuD / Plasmid: pMR21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07822
#2: Chemical ChemComp-DEF / DEFEROXAMINE MESYLATE FE(III) COMPLEX


Mass: 721.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H49FeN6O11S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
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: SSRL / Beamline: BL7-1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.97→30 Å / Num. all: 25748 / Num. obs: 22886 / % possible obs: 88.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 99.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.8
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 97.8 % / Rmerge(I) obs: 0.205 / % possible all: 88.9
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EFD

1efd


Resolution: 1.97→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / Stereochemistry target values: MAXIMUM LIKELYHOOD FUNCTION
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1097 -random
Rwork0.22 ---
all-25748 --
obs-22886 88.9 %-
Refinement stepCycle: LAST / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 35 110 2165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it0.586
X-RAY DIFFRACTIONc_mcangle_it1.038
X-RAY DIFFRACTIONc_bond_d0.702
X-RAY DIFFRACTIONc_angle_d1.098
LS refinement shellResolution: 1.97→2.04 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.241 1097 -
Rwork0.22 --
obs-24812 96.4 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Rfactor obs: 0.22 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.22

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