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- PDB-2why: Crystal structure of the triscatecholate siderophore binding prot... -

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Basic information

Entry
Database: PDB / ID: 2why
TitleCrystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis complexed with Ferri-Bacillibactin
Components
  • BACILLIBACTIN
  • Iron-uptake system-binding protein
KeywordsTRANSPORT PROTEIN / BACILLIBACTIN AND ENTEROBACTIN BINDING / TRISCATECHOLATE BINDING PROTEIN / IRON TRANSPORT / HIGH AFFINITY IRON IMPORT / IRON / MEMBRANE / PALMITATE / TRANSPORT / ABC-TYPE TRANSPORTER BINDING PROTEIN / SIDEROPHORE BINDING PROTEIN / LIPOPROTEIN / CELL MEMBRANE / ION TRANSPORT
Function / homology
Function and homology information


iron ion transport / outer membrane-bounded periplasmic space / membrane raft / plasma membrane / cytoplasm
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
: / Iron-uptake system-binding protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
BACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPeuckert, F. / Miethke, M. / Albrecht, A.G. / Essen, L.-O. / Marahiel, M.A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Structural Basis and Stereochemistry of Triscatecholate Siderophore Binding by Feua.
Authors: Peuckert, F. / Miethke, M. / Albrecht, A.G. / Essen, L.-O. / Marahiel, M.A.
History
DepositionMay 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 28, 2011Group: Other
Revision 2.0Dec 13, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 3.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-uptake system-binding protein
B: BACILLIBACTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,09314
Polymers35,6472
Non-polymers44612
Water2,630146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-89.08 kcal/mol
Surface area11910 Å2
MethodPISA
2
A: Iron-uptake system-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,13712
Polymers34,7471
Non-polymers39011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: BACILLIBACTIN
hetero molecules


  • defined by author
  • 957 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)9572
Polymers9011
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.530, 63.140, 55.530
Angle α, β, γ (deg.)90.00, 110.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Iron-uptake system-binding protein


Mass: 34746.660 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: feuA, BSU01630 / Plasmid: POK01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40409
#2: Protein/peptide BACILLIBACTIN


Mass: 900.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS SUBTILIS (bacteria)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.86 Å3/Da / Density % sol: 33.74 % / Description: NONE
Crystal growpH: 5.2
Details: PROTEIN WAS CRYSTALLIZED FROM 30% (V/V) PEG 600, 100 MM PHOSPHATE-CITRATE, PH 5.2; THEN SOAKED IN MOTHER LIQUOR CONTAINING 30% (V/V) GLYCEROL FOR CRYO PROTECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9184
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 24, 2008 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→19.76 Å / Num. obs: 28022 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.416 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PHZ

2phz


Resolution: 1.7→19.51 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.9 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 2472 8.8 %RANDOM
Rwork0.15749 ---
obs0.16042 25537 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.57 Å2
2---1.08 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 12 146 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222300
X-RAY DIFFRACTIONr_bond_other_d0.0010.021510
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9933110
X-RAY DIFFRACTIONr_angle_other_deg0.86433745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0965299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6726.4281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.408153
X-RAY DIFFRACTIONr_chiral_restr0.0640.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined0.210.2528
X-RAY DIFFRACTIONr_nbd_other0.1860.21646
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21168
X-RAY DIFFRACTIONr_nbtor_other0.1570.21158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.551.51512
X-RAY DIFFRACTIONr_mcbond_other0.1361.5594
X-RAY DIFFRACTIONr_mcangle_it0.8522374
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.453888
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2754.5733
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 213 -
Rwork0.231 1863 -
obs--99.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35950.44530.10322.9162-0.16242.5314-0.13890.24510.055-0.63680.1399-0.0088-0.07780.004-0.0010.0234-0.063-0.0052-0.04940.0097-0.1273-0.5968-6.6227-24.6814
23.2009-1.92045.13497.0403-9.779822.2577-0.26570.12590.15170.1789-0.1783-0.7507-0.79380.85950.444-0.16-0.0865-0.0177-0.051300.058815.8551-2.0074-9.6226
30.56010.26360.22292.4838-1.16511.9445-0.0046-0.0328-0.08980.1670.0349-0.03470.04330.0207-0.0302-0.0880.02390.0118-0.0646-0.0108-0.05030.8233-17.3285-0.5295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 142
2X-RAY DIFFRACTION2A143 - 165
3X-RAY DIFFRACTION3A166 - 297

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