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- PDB-5lwh: CeuE (Y288F variant) a periplasmic protein from Campylobacter jejuni. -

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Basic information

Entry
Database: PDB / ID: 5lwh
TitleCeuE (Y288F variant) a periplasmic protein from Campylobacter jejuni.
ComponentsEnterochelin ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / Periplasmic / Iron-Uptake / Tetradentate / Siderophore / mutation
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
: / Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWilde, E.J. / Blagova, E. / Hughes, A. / Raines, D.J. / Moroz, O.V. / Turkenburg, J. / 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: PDBE / 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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0433
Polymers31,9121
Non-polymers1312
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-36 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.521, 65.521, 145.654
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Enterochelin ABC transporter substrate-binding protein


Mass: 31911.822 Da / Num. of mol.: 1 / Mutation: Y288F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A0N86_06545, A0N87_06800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1J6QJN8, UniProt: Q0P8Q4*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.01M ZnCl2; 0.1M MES, pH 6.0; 20% Peg 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.47→56.81 Å / Num. obs: 62481 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.7
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.267 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.635 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKW

3zkw


Resolution: 1.47→56.81 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.971 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16196 3114 5 %RANDOM
Rwork0.12843 ---
obs0.1301 59367 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.628 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.47→56.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 2 186 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192296
X-RAY DIFFRACTIONr_bond_other_d0.0020.022225
X-RAY DIFFRACTIONr_angle_refined_deg2.4561.9853110
X-RAY DIFFRACTIONr_angle_other_deg1.36235197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77926.93998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8715437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.16154
X-RAY DIFFRACTIONr_chiral_restr0.1890.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212535
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02398
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_it3.3172.3221164
X-RAY DIFFRACTIONr_mcbond_other3.3182.321163
X-RAY DIFFRACTIONr_mcangle_it3.8723.5011457
X-RAY DIFFRACTIONr_mcangle_other3.8713.5031458
X-RAY DIFFRACTIONr_scbond_it6.8922.811132
X-RAY DIFFRACTIONr_scbond_other6.8952.811132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6494.0111649
X-RAY DIFFRACTIONr_long_range_B_refined6.6329.2742592
X-RAY DIFFRACTIONr_long_range_B_other6.63528.9532560
X-RAY DIFFRACTIONr_rigid_bond_restr6.03834520
X-RAY DIFFRACTIONr_sphericity_free26.0245126
X-RAY DIFFRACTIONr_sphericity_bonded15.53154545
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 233 -
Rwork0.235 4329 -
obs--99.96 %

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