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- PDB-1efd: PERIPLASMIC FERRIC SIDEROPHORE BINDING PROTEIN FHUD COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 1efd
TitlePERIPLASMIC FERRIC SIDEROPHORE BINDING PROTEIN FHUD COMPLEXED WITH GALLICHROME
ComponentsFERRICHROME-BINDING PERIPLASMIC PROTEIN
KeywordsMETAL TRANSPORT / periplasmic binding protein-siderophore complex / FhuD complex with gallichrome / Escherichia coli / ferric siderophore binding protein
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
GALLICHROME / Iron(3+)-hydroxamate-binding protein FhuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsClarke, T.E. / Ku, S.-Y. / Dougan, D.R. / Vogel, H.J. / Tari, L.W.
CitationJournal: 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
DepositionFeb 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: 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_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

Downloads & links

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Assembly

Deposited unit
N: FERRICHROME-BINDING PERIPLASMIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4652
Polymers29,6801
Non-polymers7841
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.54, 86.54, 91.77
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: 29680.176 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-GCR / GALLICHROME


Mass: 784.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H44GaN9O13
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.6 M Na/K phosphate, 100 mM HEPES, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
20.8 Msodium potassium phosphate1drop
30.1 MHEPES1drop
41.6 Msodium potassium phosphate1reservoir
50.2 MHEPES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11381
21381
31381
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X8C11.19387
SYNCHROTRONNSLS X8C21.19302
SYNCHROTRONNSLS X8C31.17098
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.193871
21.193021
31.170981
ReflectionResolution: 1.9→30 Å / Num. all: 60580 / Num. obs: 55765 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 99.8 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 30.1
Reflection shellResolution: 1.9→30 Å / Redundancy: 99.4 % / Rmerge(I) obs: 0.152 / Num. unique all: 54718 / % possible all: 93

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.9→20 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: CHARM
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2612 -RANDOM
Rwork0.218 ---
all-54718 --
obs-52106 93 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 49 114 2183
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 1 / Rfactor obs: 0.218 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.453
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d22.77
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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