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- PDB-5mbu: CeuE (H227A, Y288F variant) a periplasmic protein from Campylobac... -

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Basic information

Entry
Database: PDB / ID: 5mbu
TitleCeuE (H227A, Y288F variant) a periplasmic protein from Campylobacter jejuni
Components(Enterochelin uptake periplasmic binding protein) x 2
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: 1.81 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)95,9973
Polymers95,9973
Non-polymers00
Water1,964109
1
A: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)31,9991
Polymers31,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)31,9991
Polymers31,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enterochelin uptake periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)31,9991
Polymers31,9991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.900, 62.611, 67.792
Angle α, β, γ (deg.)82.23, 76.96, 75.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Enterochelin uptake periplasmic binding protein


Mass: 31998.920 Da / Num. of mol.: 2 / Mutation: H227A Y288F
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: Protein Enterochelin uptake periplasmic binding protein


Mass: 31998.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ceuE, Cj1355 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q0P8Q4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: =0.1M SPG, pH 9.0; 25% Peg1500.

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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: 1.81→65.8 Å / Num. obs: 77003 / % possible obs: 95.9 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.8
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.599 / % possible all: 96.2

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Processing

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

3zkw


Resolution: 1.81→65.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.096 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23858 3731 4.8 %RANDOM
Rwork0.19955 ---
obs0.20147 73272 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-1.97 Å2-0.43 Å2
2---0.55 Å20.78 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.81→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6295 0 0 109 6404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196438
X-RAY DIFFRACTIONr_bond_other_d0.0050.026269
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9818724
X-RAY DIFFRACTIONr_angle_other_deg1.167314394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50426.58231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.989151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.21159
X-RAY DIFFRACTIONr_chiral_restr0.1230.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217340
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021311
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_it3.3563.4733437
X-RAY DIFFRACTIONr_mcbond_other3.3543.4723436
X-RAY DIFFRACTIONr_mcangle_it4.4765.1924286
X-RAY DIFFRACTIONr_mcangle_other4.4775.1934287
X-RAY DIFFRACTIONr_scbond_it3.6743.6473001
X-RAY DIFFRACTIONr_scbond_other3.6743.6473001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2825.3334430
X-RAY DIFFRACTIONr_long_range_B_refined6.44641.0416889
X-RAY DIFFRACTIONr_long_range_B_other6.44741.0336880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 289 -
Rwork0.31 5417 -
obs--96.08 %

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