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- PDB-5oah: THE PERIPLASMIC BINDING PROTEIN CEUE OF CAMPYLOBACTER JEJUNI BIND... -

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Basic information

Entry
Database: PDB / ID: 5oah
TitleTHE PERIPLASMIC BINDING PROTEIN CEUE OF CAMPYLOBACTER JEJUNI BINDS THE IRON(III) COMPLEX OF Azotochelin
ComponentsEnterochelin ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / IRON UPTAKE / TETRADENTATE SIDEROPHORE BINDING PROTEIN / AZOTOCHELIN
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / 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
Azotochelin / : / Enterochelin ABC transporter substrate-binding protein / Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRaines, A.D.J. / Blagova, E. / Dodson, E.J. / Wilson, K.S. / Duhme-Klair, A.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Nat Catal / Year: 2018
Title: Redox-switchable siderophore anchor enables reversible artificial metalloenzyme assembly
Authors: Raines, A.D.J. / Clarke, J.E. / Blagova, E. / Dodson, E.J. / Wilson, K.S. / Duhme-Klair, A.K.
History
DepositionJun 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 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 / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,5197
Polymers95,5703
Non-polymers9484
Water2,702150
1
A: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3313
Polymers31,8571
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3313
Polymers31,8571
Non-polymers4742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Enterochelin ABC transporter substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)31,8571
Polymers31,8571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.139, 63.410, 67.674
Angle α, β, γ (deg.)82.710, 76.360, 79.030
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein Enterochelin ABC transporter substrate-binding protein


Mass: 31856.744 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: AD53_07815, BKM79_06765 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E7P069, UniProt: Q0P8Q4*PLUS
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-95B / Azotochelin


Mass: 418.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.5 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5 / Details: 0.2M NaF 20% PEG3350 Fe-Azotochelin stock solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→65.52 Å / Num. obs: 84430 / % possible obs: 99.1 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1 / CC1/2: 0.589 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zkw

3zkw


Resolution: 1.8→65.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4314 5.1 %RANDOM
Rwork0.2047 80097 --
obs0.207 84411 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.96 Å2 / Biso mean: 39.161 Å2 / Biso min: 19.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å2-1.05 Å20.91 Å2
2---0.29 Å22.39 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→65.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6729 0 62 150 6941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196902
X-RAY DIFFRACTIONr_bond_other_d00.026760
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9879291
X-RAY DIFFRACTIONr_angle_other_deg3.7692.99315782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.79226.609289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.339151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3471512
X-RAY DIFFRACTIONr_chiral_restr0.1220.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217506
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021188
X-RAY DIFFRACTIONr_mcbond_it3.4933.6223453
X-RAY DIFFRACTIONr_mcbond_other3.4933.6213452
X-RAY DIFFRACTIONr_mcangle_it4.625.424311
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 312 -
Rwork0.318 5872 -
all-6184 -
obs--98.03 %

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