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- PDB-1k7s: FhuD complexed with albomycin-delta 2 -

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Basic information

Entry
Database: PDB / ID: 1k7s
TitleFhuD complexed with albomycin-delta 2
ComponentsFerrichrome-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / two mixed domains connected by an alpha helix
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
DELTA-2-ALBOMYCIN A1 / Iron(3+)-hydroxamate-binding protein FhuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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.R. / Vogel, H.J. / Tari, L.W.
History
DepositionOct 21, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)30,6552
Polymers29,6091
Non-polymers1,0461
Water68538
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, 91.60
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: 29609.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pMR21 / Production host: Escherichia coli (E. coli) / References: UniProt: P07822
#2: Chemical ChemComp-ALB / DELTA-2-ALBOMYCIN A1


Mass: 1045.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H57FeN12O18S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 16% PEG 4000, 0.1M Na acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.3 mg/mlprotein1drop
28 %PEG40001drop
30.05 Msodium acetate1droppH5.2
416 %PEG40001reservoir
50.1 Msodium acetate1reservoirpH5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 20, 2000 / Details: Osmic confocal multilayer optics
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 11873 / Num. obs: 10715 / % possible obs: 90.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 94.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 95.5 % / Rmerge(I) obs: 0.646 / % possible all: 90.2
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 94.8 % / Rmerge(I) obs: 0.0099
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.6

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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: 2.6→30 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: mlf
RfactorNum. reflection% reflectionSelection details
Rfree0.243 484 -random
obs0.194 10715 90.2 %-
all-11873 --
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 41 38 2092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007144
X-RAY DIFFRACTIONc_angle_d1.36891
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.194 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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