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- PDB-4fna: Structure of unliganded FhuD2 from Staphylococcus Aureus -

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Basic information

Entry
Database: PDB / ID: 4fna
TitleStructure of unliganded FhuD2 from Staphylococcus Aureus
ComponentsFerric hydroxamate receptor 2
KeywordsMETAL BINDING PROTEIN / Class III Solute Binding Protein / transport of hydroxamate siderophores / FhuCBG / membrane-bound
Function / homology
Function and homology information


iron coordination entity transport / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsShilton, B.H. / Heinrichs, D.E.
CitationJournal: Biochemistry / Year: 2014
Title: Crystal and solution structure analysis of FhuD2 from Staphylococcus aureus in multiple unliganded conformations and bound to ferrioxamine-B.
Authors: Podkowa, K.J. / Briere, L.A. / Heinrichs, D.E. / Shilton, B.H.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Ferric hydroxamate receptor 2
B: Ferric hydroxamate receptor 2
C: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,10016
Polymers94,8513
Non-polymers1,24913
Water00
1
A: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8093
Polymers31,6171
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,57811
Polymers31,6171
Non-polymers96110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7132
Polymers31,6171
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)207.507, 207.507, 162.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Ferric hydroxamate receptor 2


Mass: 31617.119 Da / Num. of mol.: 3 / Fragment: UNP residues 25-302
Source method: isolated from a genetically manipulated source
Details: expressed as GST fusion; GST removed using TEV protease
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: fhud2 / Plasmid: pMTS57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BGA5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.37 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M glycine, 3.5 to 3.8 M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 28, 2002
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.5→24.714 Å / Num. all: 22693 / Num. obs: 22690 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 141 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.7
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.222 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX1.8_1069refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4FKM

4fkm


Resolution: 3.5→24.714 Å / SU ML: 0.38 / σ(F): 1.33 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 1077 4.87 %
Rwork0.2201 --
obs0.2232 22125 97.84 %
all-22624 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.9 Å2
Baniso -1Baniso -2Baniso -3
1--23.419 Å2-23.419 Å246.839 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→24.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 65 0 6683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116796
X-RAY DIFFRACTIONf_angle_d1.5689143
X-RAY DIFFRACTIONf_dihedral_angle_d17.9252595
X-RAY DIFFRACTIONf_chiral_restr0.086971
X-RAY DIFFRACTIONf_plane_restr0.0071143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-3.65890.35081410.29582538X-RAY DIFFRACTION96
3.6589-3.85110.3761370.2652530X-RAY DIFFRACTION96
3.8511-4.09140.29191350.23322569X-RAY DIFFRACTION96
4.0914-4.40570.25391310.20982588X-RAY DIFFRACTION98
4.4057-4.8460.30661380.20482619X-RAY DIFFRACTION98
4.846-5.54030.29481140.2212690X-RAY DIFFRACTION99
5.5403-6.95440.32541150.24462739X-RAY DIFFRACTION100
6.9544-24.71480.22691660.18932775X-RAY DIFFRACTION99

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