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- PDB-4aiq: The FrpB iron transporter from Neisseria meningitidis (F5-1 variant) -

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Basic information

Entry
Database: PDB / ID: 4aiq
TitleThe FrpB iron transporter from Neisseria meningitidis (F5-1 variant)
ComponentsFERRIC ENTEROBACTIN RECEPTOR
KeywordsTRANSPORT PROTEIN / OUTER MEMBRANE / TONB-DEPENDENT TRANSPORTER
Function / homology
Function and homology information


TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / Maltoporin; Chain A / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSaleem, M. / Prince, S.M. / Derrick, J.P.
Citation
Journal: Plos One / Year: 2013
Title: Use of a Molecular Decoy to Segregate Transport from Antigenicity in the Frpb Iron Transporter from Neisseria Meningitidis
Authors: Saleem, M. / Prince, S.M. / Rigbb, S.E.J. / Imran, M. / Patel, H. / Chan, H. / Sanders, H. / Maiden, M.C.J. / Feavers, I.M. / Derrick, J.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Refolding, Purification and Crystallization of the Frpb Outer Membrane Iron Transporter from Neisseria Meningitidis.
Authors: Saleem, M. / Prince, S.M. / Patel, H. / Chan, H. / Feavers, I.M. / Derrick, J.P.
History
DepositionFeb 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references / Structure summary
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: 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: FERRIC ENTEROBACTIN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8363
Polymers82,7111
Non-polymers1252
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.980, 78.690, 73.430
Angle α, β, γ (deg.)90.00, 97.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FERRIC ENTEROBACTIN RECEPTOR


Mass: 82710.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Variant: F5-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7 EXPRESS / References: UniProt: F0N0E1
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 6.5
Details: 30 MM DI-ETHYLENE GLYCOL, 30 MM TRI-ETHYLENE GLYCOL, 30 MM TETRA-ETHYLENE GLYCOL, 30 MM PENTA-ETHYLENE GLYCOL, 45 MM IMIDAZOLE, 20% (W/V) PEGMME550, 10% (W/V) PEG 20000 AND 56 MM MES (PH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969
DetectorType: DECTIS PILATUS / Detector: PIXEL / Date: Oct 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.6→36 Å / Num. obs: 29989 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AIP

4aip


Resolution: 2.6→36.42 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / SU B: 11.193 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IDENTITY OF THE BOUND FE CONFIRMED FROM ANOMALOUS DIFFRACTION DATA COLLECTED AT 1.74A FROM THE SAME CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.27749 1506 5 %RANDOM
Rwork0.22654 ---
obs0.22918 28422 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-2.92 Å2
2--0.34 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 6 44 5218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0215284
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.161.9327135
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3765657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6923.82267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90915869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3671539
X-RAY DIFFRACTIONr_chiral_restr0.150.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214117
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0391.53249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01925187
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.25732035
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3864.51948
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 101 -
Rwork0.317 2104 -
obs--98.53 %

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