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- PDB-5a5d: A complex of the synthetic siderophore analogue Fe(III)-5-LICAM w... -

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Basic information

Entry
Database: PDB / ID: 5a5d
TitleA complex of the synthetic siderophore analogue Fe(III)-5-LICAM with the CeuE periplasmic protein from Campylobacter jejuni
ComponentsENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / SYNTHETIC SIDEROPHORE / LIGAND COMPLEX / PERIPLASMIC BINDING PROTEIN / TETRADENTATE SIDEROPHORES
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
FatB domain / : / 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
N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide) / : / Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsBlagova, E. / Hughes, A. / Moroz, O.V. / Raines, D.J. / Wilde, E.J. / Turkenburg, J.P. / Duhme-Klair, A.-K. / Wilson, K.S.
CitationJournal: Sci Rep / Year: 2017
Title: Interactions of the periplasmic binding protein CeuE with Fe(III) n-LICAM(4-) siderophore analogues of varied linker length.
Authors: Wilde, E.J. / Hughes, A. / Blagova, E.V. / Moroz, O.V. / Thomas, R.P. / Turkenburg, J.P. / Raines, D.J. / Duhme-Klair, A.K. / Wilson, K.S.
History
DepositionJun 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references / Structure summary
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Apr 19, 2017Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3583
Polymers31,9281
Non-polymers4302
Water4,738263
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.520, 67.510, 69.520
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 ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN CEUE


Mass: 31927.822 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0P8Q4
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-5LC / N,N'-pentane-1,5-diylbis(2,3-dihydroxybenzamide)


Mass: 374.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL TRUNCATION, FIRST TWO RESIDUES ALA22 AND MET23 ARE REMAINING FROM THE PLASMID AFTER ...N-TERMINAL TRUNCATION, FIRST TWO RESIDUES ALA22 AND MET23 ARE REMAINING FROM THE PLASMID AFTER HISTIDINE TAG CLEAVAGE

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: PACT H12, 0.2M SODIUM MALONATE, 0.1M BIS-TRIS-PROPANE PH 8.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.74→46.07 Å / Num. obs: 30349 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.74→46.07 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.22 1536 5.1 %
Rwork0.175 --
obs0.177 30349 98 %
Refinement stepCycle: LAST / Resolution: 1.74→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 28 263 2511

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