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- PDB-5od5: Periplasmic binding protein CeuE complexed with a synthetic catalyst -

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Basic information

Entry
Database: PDB / ID: 5od5
TitlePeriplasmic binding protein CeuE complexed with a synthetic catalyst
ComponentsEnterochelin ABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / CeuE / mettalloenzeyme / Synthetic catalyst / sidephore
Function / homology
Function and homology information


iron ion 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
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / Azotochelin / Chem-9RT / : / : / PHOSPHATE ION / Chem-RIR / 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: 1.9 Å
AuthorsDuhme-Klair, A.K. / Raines, D.J. / Clarke, J.E. / Blagova, E.V. / Dodson, E.J. / Wilson, K.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L024829/1 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
DepositionJul 4, 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 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)99,60722
Polymers95,5703
Non-polymers4,03719
Water2,108117
1
A: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2237
Polymers31,8571
Non-polymers1,3666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9697
Polymers31,8571
Non-polymers1,1126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Enterochelin ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4158
Polymers31,8571
Non-polymers1,5587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.692, 62.759, 68.195
Angle α, β, γ (deg.)87.380, 76.900, 79.270
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Enterochelin ABC transporter substrate-binding protein / Ceue with Redox-switchable siderophore


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

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Non-polymers , 8 types, 136 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ir
#4: Chemical ChemComp-95B / Azotochelin


Mass: 418.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O8
#5: Chemical ChemComp-9RT / 4-(aminomethyl)-~{N}-(pyridin-2-ylmethyl)benzenesulfonamide


Mass: 277.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N3O2S
#6: Chemical ChemComp-RIR / [(1,2,3,4,5-Eta)-1,2,3,4,5-Pentamethylcyclopentadienyl]iridium(III)


Mass: 327.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15Ir
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O9
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 0.1M succinic acid, sodium dihydrogen phosphate, glycine. 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→66.42 Å / Num. obs: 83133 / % possible obs: 97.9 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.622 / CC1/2: 0.502 / % possible all: 100

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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 / Resolution: 1.9→66.42 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.14
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 3437 4.9 %RANDOM
Rwork0.1766 ---
obs0.1789 70601 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.14 Å2 / Biso mean: 44.1571 Å2 / Biso min: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-0.43 Å20.27 Å2
2--2.29 Å20.23 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→66.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6729 0 164 117 7010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197019
X-RAY DIFFRACTIONr_bond_other_d00.026852
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9879424
X-RAY DIFFRACTIONr_angle_other_deg3.712.98315976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63326.033300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.256151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191512
X-RAY DIFFRACTIONr_chiral_restr0.1180.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217568
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021206
X-RAY DIFFRACTIONr_mcbond_it3.8284.0863458
X-RAY DIFFRACTIONr_mcbond_other3.8284.0853457
X-RAY DIFFRACTIONr_mcangle_it5.1286.1084319
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 270 -
Rwork0.268 4943 -
all-5213 -
obs--99.81 %

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