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- PDB-4fil: Structure of FhuD2 from Staphylococcus Aureus with Bound Ferrioxa... -

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Basic information

Entry
Database: PDB / ID: 4fil
TitleStructure of FhuD2 from Staphylococcus Aureus with Bound Ferrioxamine B
ComponentsFerric hydroxamate receptor 2
KeywordsMETAL BINDING PROTEIN / Class III Solute Binding Protein / primary binding site for iron-hydroxamate siderophores / FhuCBG / extracellular
Function / homology
Function and homology information


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
Ferrioxamine B / Similar to ferric hydroxamate receptor 1 / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBriere, L.K. / 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 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
D: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,06076
Polymers117,1984
Non-polymers6,86272
Water8,611478
1
A: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,13921
Polymers29,2991
Non-polymers1,84020
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,14621
Polymers29,2991
Non-polymers1,84620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,69814
Polymers29,2991
Non-polymers1,39813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ferric hydroxamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,07720
Polymers29,2991
Non-polymers1,77819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.343, 78.996, 116.811
Angle α, β, γ (deg.)90.00, 109.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ferric hydroxamate receptor 2


Mass: 29299.451 Da / Num. of mol.: 4 / Fragment: UNP residues 44-302 / Mutation: K117A, K118A, K121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: fhud2, SAV2284 / Plasmid: pGEX-FhuD2(delta)43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BGA5, UniProt: A0A0H3JWU6*PLUS
#2: Chemical
ChemComp-0UE / Ferrioxamine B


Mass: 613.505 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H45FeN6O8
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.9 M NaCl, 100 mM imidazole, 250 mM Zn(OAc)2, 30 mg/mL FhuD2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: May 3, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection twinType: pseudo-merohedral / Operator: -h,-k,h+l / Fraction: 0.33
ReflectionResolution: 2.4→45 Å / Num. all: 54573 / Num. obs: 50153 / % possible obs: 91.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6402 / % possible all: 81.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FKM

4fkm


Resolution: 2.4→45 Å / Isotropic thermal model: Isotropic / σ(F): 1.37 / Phase error: 33 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2631 5.25 %random
Rwork0.1976 ---
obs0.2013 50142 91.74 %-
all-54573 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8124 0 264 478 8866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028496
X-RAY DIFFRACTIONf_angle_d0.67311440
X-RAY DIFFRACTIONf_dihedral_angle_d14.083436
X-RAY DIFFRACTIONf_chiral_restr0.0491200
X-RAY DIFFRACTIONf_plane_restr0.0031428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.44630.44221190.30392152X-RAY DIFFRACTION72
2.4463-2.49620.36921330.28782352X-RAY DIFFRACTION78
2.4962-2.55040.37951240.27742462X-RAY DIFFRACTION81
2.5504-2.60970.32791190.26832483X-RAY DIFFRACTION83
2.6097-2.67490.3521200.26482495X-RAY DIFFRACTION83
2.6749-2.74720.28781320.25442486X-RAY DIFFRACTION83
2.7472-2.82790.32461280.24142556X-RAY DIFFRACTION84
2.8279-2.91910.2711590.23482536X-RAY DIFFRACTION84
2.9191-3.02330.25891510.22622567X-RAY DIFFRACTION85
3.0233-3.14420.27871300.22612652X-RAY DIFFRACTION87
3.1442-3.2870.25481400.20792711X-RAY DIFFRACTION90
3.287-3.460.22921530.20392749X-RAY DIFFRACTION91
3.46-3.67630.21551570.17952819X-RAY DIFFRACTION93
3.6763-3.95930.18981220.16452907X-RAY DIFFRACTION96
3.9593-4.35630.16121530.15372897X-RAY DIFFRACTION95
4.3563-4.98330.15581590.14972880X-RAY DIFFRACTION95
4.9833-6.26560.17391330.17422954X-RAY DIFFRACTION96
6.2656-27.09650.21091790.2112936X-RAY DIFFRACTION94

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