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- PDB-5adw: The Periplasmic Binding Protein CeuE of Campylobacter jejuni pref... -

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Basic information

Entry
Database: PDB / ID: 5adw
TitleThe Periplasmic Binding Protein CeuE of Campylobacter jejuni preferentially binds the iron(III) complex of the Linear Dimer Component of Enterobactin
ComponentsENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / ENTEROBACTIN UPTAKE / IRON / SIDEROPHORE / BINDING PROTEIN / TETRADENTATE
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
Chem-EHS / : / Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRaines, D.J. / Moroz, O.V. / Turkenburg, J.P. / Wilson, K.S. / Duhme-Klair, A.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Bacteria in an Intense Competition for Iron: Key Component of the Campylobacter Jejuni Iron Uptake System Scavenges Enterobactin Hydrolysis Product.
Authors: Raines, D.J. / Moroz, O.V. / Blagova, E.V. / Turkenburg, J.P. / Wilson, K.S. / Duhme-Klair, A.
History
DepositionAug 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,50711
Polymers95,1773
Non-polymers1,3318
Water2,342130
1
A: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4025
Polymers31,7261
Non-polymers6764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8603
Polymers31,7261
Non-polymers1342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2463
Polymers31,7261
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.461, 63.021, 67.011
Angle α, β, γ (deg.)83.36, 76.57, 78.24
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 24 - 310 / Label seq-ID: 1 - 287

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN / CEUE


Mass: 31725.551 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 44-330
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL TRUNCATION / Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0P8Q4
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EHS / 2S-2-[(2,3-DIHYDROXYPHENYL)CARBONYLAMINO]-3-[(2S)-2-[(2,3-DIHYDROXYPHENYL)CARBONYLAMINO]-3-HYDROXY-PROPANOYL]OXY-PROPANOIC ACID


Mass: 464.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N2O11
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.48 Å3/Da / Density % sol: 50.46 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M MMT (DL-MALIC ACID, MES, TRIS, 1:2:2) BUFFER, PH 8.0, 25% (W/V) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→45.76 Å / Num. obs: 70279 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKW

3zkw


Resolution: 1.9→65.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.528 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26407 3495 5 %RANDOM
Rwork0.2248 ---
obs0.22676 66562 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.232 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å2-1.62 Å20.39 Å2
2---1.11 Å20.99 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6581 0 81 130 6792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196761
X-RAY DIFFRACTIONr_bond_other_d0.0080.026697
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9959142
X-RAY DIFFRACTIONr_angle_other_deg1.39315439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44926.679271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.108151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8551512
X-RAY DIFFRACTIONr_chiral_restr0.1040.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217611
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021373
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_it3.9544.0923441
X-RAY DIFFRACTIONr_mcbond_other3.9544.0913440
X-RAY DIFFRACTIONr_mcangle_it5.3156.1224296
X-RAY DIFFRACTIONr_mcangle_other5.3146.1224297
X-RAY DIFFRACTIONr_scbond_it4.4154.4163320
X-RAY DIFFRACTIONr_scbond_other4.4144.4173321
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3046.4674847
X-RAY DIFFRACTIONr_long_range_B_refined8.08332.0917512
X-RAY DIFFRACTIONr_long_range_B_other8.08232.0967513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A169410.11
12B169410.11
21A173850.1
22C173850.1
31B169070.12
32C169070.12
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 244 -
Rwork0.356 4790 -
obs--94.95 %

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