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- PDB-5ad1: A complex of the synthetic siderophore analogue Fe(III)-8-LICAM w... -

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Basic information

Entry
Database: PDB / ID: 5ad1
TitleA complex of the synthetic siderophore analogue Fe(III)-8-LICAM with the CeuE periplasmic protein from Campylobacter jejuni
ComponentsENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
KeywordsMETAL BINDING 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'-OCTANE-1,8-DIYLBIS(2,3-DIHYDROXYBENZAMIDE) / : / Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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
DepositionAug 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)32,4973
Polymers32,0251
Non-polymers4722
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.980, 55.980, 140.080
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: 32024.936 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 44-330
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-8LC / N,N'-OCTANE-1,8-DIYLBIS(2,3-DIHYDROXYBENZAMIDE)


Mass: 416.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL TRUNCATION. PRO, ALA AND MET FROM CLONING

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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: 2.63 Å3/Da / Density % sol: 53.25 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M SODIUM FORMATE, 0.1M BTP BUFFER, PH 8.5, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.32→55.98 Å / Num. obs: 77761 / % possible obs: 96.6 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 1.32→1.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.3 / % possible all: 76

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A5V

5a5v


Resolution: 1.32→55.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.828 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18056 3815 4.9 %RANDOM
Rwork0.14001 ---
obs0.14195 73860 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.926 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.32→55.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 31 397 2667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192377
X-RAY DIFFRACTIONr_bond_other_d0.0010.022383
X-RAY DIFFRACTIONr_angle_refined_deg1.961.9993227
X-RAY DIFFRACTIONr_angle_other_deg0.98835514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30826.86999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81215449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.188154
X-RAY DIFFRACTIONr_chiral_restr0.1330.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5841.0751184
X-RAY DIFFRACTIONr_mcbond_other1.5841.0731183
X-RAY DIFFRACTIONr_mcangle_it1.8671.6261485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.361.3641193
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.77234760
X-RAY DIFFRACTIONr_sphericity_free23.585564
X-RAY DIFFRACTIONr_sphericity_bonded9.7855061
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 212 -
Rwork0.254 4237 -
obs--75.84 %

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