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

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Basic information

Entry
Database: PDB / ID: 5tcy
TitleA complex of the synthetic siderophore analogue Fe(III)-5-LICAM with CeuE (H227L variant), a periplasmic protein from Campylobacter jejuni.
ComponentsEnterochelin uptake periplasmic binding protein
KeywordsMETAL TRANSPORT / Periplasmic / Iron-Uptake / Tetradentate / Siderophore
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 BJ-CJGB96299 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWilde, E.J. / Blagova, E. / Hughes, A. / Raines, D.J. / Moroz, O.V. / Turkenburg, J.P. / Duhme-Klair, A.-K. / Wilson, K.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L024829/1 United Kingdom
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
DepositionSep 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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
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_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enterochelin uptake periplasmic binding protein
B: Enterochelin uptake periplasmic binding protein
C: Enterochelin uptake periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4629
Polymers96,1713
Non-polymers1,2916
Water3,009167
1
A: Enterochelin uptake periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4873
Polymers32,0571
Non-polymers4302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin uptake periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4873
Polymers32,0571
Non-polymers4302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enterochelin uptake periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4873
Polymers32,0571
Non-polymers4302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.696, 62.881, 69.867
Angle α, β, γ (deg.)82.09, 74.67, 77.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Enterochelin uptake periplasmic binding protein


Mass: 32056.998 Da / Num. of mol.: 3 / Mutation: H227L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni BJ-CJGB96299 (Campylobacter)
Gene: K680_0601 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W8LI20, UniProt: Q0P8Q4*PLUS
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: C19H22N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.53 Å3/Da / Density % sol: 51.33 % / Description: Rod shaped crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M PCB buffer, pH 8, 25% PEG 1500 +cryo 33% PEG 1500 in well solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2016
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→67.13 Å / Num. obs: 70811 / % possible obs: 95.9 % / Redundancy: 3.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.418 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKW

3zkw


Resolution: 1.9→67.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.069 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21499 3451 4.9 %RANDOM
Rwork0.17143 ---
obs0.17355 67360 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å2-0.79 Å20.14 Å2
2---0.75 Å21.23 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6586 0 84 167 6837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196826
X-RAY DIFFRACTIONr_bond_other_d0.0020.026848
X-RAY DIFFRACTIONr_angle_refined_deg1.852.0029232
X-RAY DIFFRACTIONr_angle_other_deg1.041315785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07826.55258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.013151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5911513
X-RAY DIFFRACTIONr_chiral_restr0.1140.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217689
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021396
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_it2.8583.2673485
X-RAY DIFFRACTIONr_mcbond_other2.8583.2673484
X-RAY DIFFRACTIONr_mcangle_it3.7984.8864356
X-RAY DIFFRACTIONr_mcangle_other3.7984.8874357
X-RAY DIFFRACTIONr_scbond_it4.1493.6593341
X-RAY DIFFRACTIONr_scbond_other4.1483.663342
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2775.2794872
X-RAY DIFFRACTIONr_long_range_B_refined7.32639.0067478
X-RAY DIFFRACTIONr_long_range_B_other7.3338.9697461
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 297 -
Rwork0.293 4889 -
obs--95.95 %

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