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- PDB-5mbq: CeuE (H227A variant) a periplasmic protein from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 5mbq
TitleCeuE (H227A variant) a periplasmic protein from Campylobacter jejuni
ComponentsEnterochelin uptake periplasmic binding protein
KeywordsMETAL TRANSPORT / Periplasmic / Iron-Uptake / Tetradentate / Siderophore / mutation
Function / homology
Function and homology information


iron ion transport / 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: 1.33 Å
AuthorsWilde, E.J. / Blagova, E.V. / 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
DepositionNov 8, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)96,0453
Polymers96,0453
Non-polymers00
Water9,422523
1
A: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)32,0151
Polymers32,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)32,0151
Polymers32,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)32,0151
Polymers32,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.988, 62.682, 67.969
Angle α, β, γ (deg.)82.11, 77.21, 76.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Enterochelin uptake periplasmic binding protein


Mass: 32014.920 Da / Num. of mol.: 3 / Mutation: H227A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ceuE, Cj1355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0P8Q4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M MMT buffer, 25% Peg 1500.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.33→66.02 Å / Num. obs: 192548 / % possible obs: 65.9 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0044 / Net I/σ(I): 11.8
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 3 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.604 / % possible all: 41

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
MOLREPphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKW

3zkw


Resolution: 1.33→66.02 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.954 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.056 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19313 8932 5 %RANDOM
Rwork0.14786 ---
obs0.15013 168875 87.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.583 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å21.25 Å2-0.97 Å2
2--1.09 Å2-1.04 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.33→66.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 0 523 6947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0196656
X-RAY DIFFRACTIONr_bond_other_d0.0020.026540
X-RAY DIFFRACTIONr_angle_refined_deg2.7361.9859054
X-RAY DIFFRACTIONr_angle_other_deg1.702315085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.426.808260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.841151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6751510
X-RAY DIFFRACTIONr_chiral_restr0.20.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217598
X-RAY DIFFRACTIONr_gen_planes_other0.010.021350
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_it3.8712.2913461
X-RAY DIFFRACTIONr_mcbond_other3.832.293460
X-RAY DIFFRACTIONr_mcangle_it4.4163.4544328
X-RAY DIFFRACTIONr_mcangle_other4.4273.4544329
X-RAY DIFFRACTIONr_scbond_it5.2182.5723195
X-RAY DIFFRACTIONr_scbond_other5.2222.5733196
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6323.7214701
X-RAY DIFFRACTIONr_long_range_B_refined5.35528.6677492
X-RAY DIFFRACTIONr_long_range_B_other5.31528.3887396
X-RAY DIFFRACTIONr_rigid_bond_restr6.166313195
X-RAY DIFFRACTIONr_sphericity_free29.775346
X-RAY DIFFRACTIONr_sphericity_bonded17.9513258
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 323 -
Rwork0.255 6136 -
obs--42.81 %

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