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- PDB-5a1j: Periplasmic Binding Protein CeuE in complex with ferric 4-LICAM -

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Basic information

Entry
Database: PDB / ID: 5a1j
TitlePeriplasmic Binding Protein CeuE in complex with ferric 4-LICAM
ComponentsENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / METAL-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
: / N,N'-butane-1,4-diylbis(2,3-dihydroxybenzamide) / Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRaines, D.J. / Moroz, O.V. / Wilson, K.S. / Duhme-Klair, A.K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Interactions of a Periplasmic Binding Protein with a Tetradentate Siderophore Mimic.
Authors: Raines, D.J. / Moroz, O.V. / Wilson, K.S. / Duhme-Klair, A.
History
DepositionApr 30, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionMay 13, 2015ID: 3ZK3
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 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 / struct_conn / 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 / _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_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

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Assembly

Deposited unit
A: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2733
Polymers31,8571
Non-polymers4162
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.420, 66.890, 67.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN / CEUE


Mass: 31856.744 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TRUNCATION, RESIDUES 44-330
Source method: isolated from a genetically manipulated source
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.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-LCM / N,N'-butane-1,4-diylbis(2,3-dihydroxybenzamide) / 4-LICAM


Mass: 360.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL TRUNCATION. FIRST MET FROM CLONING

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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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M SODIUM NITRATE, 0.1M BIS TRIS PROPANE PH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9784
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.854
11-H, L, K20.146
ReflectionResolution: 1.61→44.96 Å / Num. obs: 204289 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.3
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.2 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHU

2chu


Resolution: 1.6→33.65 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.866 / SU B: 6.144 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. POOR REFINEMENT STATISTICS BECAUSE OF SPLIT SPOTS AND TWINNING
RfactorNum. reflection% reflectionSelection details
Rfree0.31242 1773 5 %RANDOM
Rwork0.26422 ---
obs0.2666 34006 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.566 Å2
Baniso -1Baniso -2Baniso -3
1--7.83 Å20 Å20 Å2
2--1.39 Å20 Å2
3---6.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 27 78 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192328
X-RAY DIFFRACTIONr_bond_other_d0.0010.022351
X-RAY DIFFRACTIONr_angle_refined_deg2.372.0013145
X-RAY DIFFRACTIONr_angle_other_deg1.0735443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3435295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21926.90797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.73615451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.236154
X-RAY DIFFRACTIONr_chiral_restr0.1320.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212610
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02472
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_it1.5491.5861159
X-RAY DIFFRACTIONr_mcbond_other1.5491.5861158
X-RAY DIFFRACTIONr_mcangle_it2.1572.3811449
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4591.6721169
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 100 -
Rwork0.29 1910 -
obs--75.28 %
Refinement TLS params.Method: refined / Origin x: 1.3942 Å / Origin y: 2.3768 Å / Origin z: 2.4774 Å
111213212223313233
T0.0664 Å20.0009 Å20.003 Å2-0.0605 Å2-0.0008 Å2--0.003 Å2
L0.1684 °20.1017 °20.0889 °2-0.1675 °20.1292 °2--0.1035 °2
S0.0071 Å °-0.0674 Å °-0.0058 Å °-0.011 Å °-0.013 Å °0.0054 Å °-0.0006 Å °-0.0196 Å °0.006 Å °

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