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- PDB-4fkm: Structure of unliganded and reductively methylated FhuD2 from sta... -

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Basic information

Entry
Database: PDB / ID: 4fkm
TitleStructure of unliganded and reductively methylated FhuD2 from staphylococcus aureus
ComponentsSimilar to ferric hydroxamate receptor 1
KeywordsMETAL BINDING PROTEIN / Class III Solute Binding Protein / membrane protein / transport of hydroxamate siderophores / Reductive methylation of lysyl residues
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space / metal ion binding
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
Similar to ferric hydroxamate receptor 1 / Similar to ferric hydroxamate receptor 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsPodkowa, K.J. / Heinrichs, D.E. / Shilton, B.H.
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 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Similar to ferric hydroxamate receptor 1
B: Similar to ferric hydroxamate receptor 1


Theoretical massNumber of molelcules
Total (without water)61,7572
Polymers61,7572
Non-polymers00
Water3,909217
1
A: Similar to ferric hydroxamate receptor 1


Theoretical massNumber of molelcules
Total (without water)30,8781
Polymers30,8781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Similar to ferric hydroxamate receptor 1


Theoretical massNumber of molelcules
Total (without water)30,8781
Polymers30,8781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.005, 75.218, 100.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Similar to ferric hydroxamate receptor 1


Mass: 30878.389 Da / Num. of mol.: 2 / Fragment: UNP residues 44-301
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: SAV2284 / Plasmid: pGEX-FhuD2(delta)43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99RY8, UniProt: A0A0H3JWU6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10 mg/mL protein concentration; 20% (w/v) PEG 3350, 25% (w/v) PEG 400, 100 mM MgCl2,100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0000, 0.9797, 0.9795, 0.9793
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 21, 2005
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97971
30.97951
40.97931
ReflectionResolution: 2.2→60.3 Å / Num. all: 26093 / Num. obs: 26198 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.7 / Num. unique all: 3669 / % possible all: 98.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→60 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2397 -random
Rwork0.216 ---
all-49269 --
obs-48669 98.8 %-
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 0 217 4484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.60897
X-RAY DIFFRACTIONc_bond_d0.006322

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