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- PDB-4b7o: THE FrpB IRON TRANSPORTER FROM NEISSERIA MENINGITIDIS (F5-1 VARIA... -

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Basic information

Entry
Database: PDB / ID: 4b7o
TitleTHE FrpB IRON TRANSPORTER FROM NEISSERIA MENINGITIDIS (F5-1 VARIANT) APOPROTEIN FORM
ComponentsIRON-REGULATED OUTER MEMBRANE PROTEIN
KeywordsTRANSPORT PROTEIN / TONB-DEPENDENT TRANSPORTER
Function / homology
Function and homology information


siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily ...TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Iron-regulated outer membrane protein
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSaleem, M. / Prince, S.M. / Derrick, J.P.
CitationJournal: 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. / Rigby, S.E.J. / Imran, M. / Patel, H. / Chan, H. / Sanders, H. / Maiden, M.C.J. / Feavers, I.M. / Derrick, J.P.
History
DepositionAug 21, 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 1.2Mar 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IRON-REGULATED OUTER MEMBRANE PROTEIN


Theoretical massNumber of molelcules
Total (without water)82,7111
Polymers82,7111
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.210, 79.100, 74.750
Angle α, β, γ (deg.)90.00, 97.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein IRON-REGULATED OUTER MEMBRANE PROTEIN / FRPB IRON TRANSPORTER


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 / Plasmid: PET30EKLIC / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): T7 EXPRESS / References: UniProt: Q841A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONFLICTS DUE TO STRAIN VARIATION

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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: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growDetails: 20MM NA L-GLUTAMATE, 20MM D, L-ALANINE, 20MM GLYCINE, 20MM LYSINE (RACEMIC), 20MM SERINE (RACEMIC), 39.8MM IMIDAZOLE, 24% (W/V) PEGMME550, 12% (W/V) PEG 20,000 AND 61.2MM MES/NAOH (PH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.32→37 Å / Num. obs: 43114 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.8
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AIQ

4aiq


Resolution: 2.32→37.05 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.223 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28067 2172 5 %RANDOM
Rwork0.23315 ---
obs0.23559 40942 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.092 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å2-3.94 Å2
2---0.38 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.32→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 0 79 5182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.025210
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9327029
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52323.91266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4215867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.821538
X-RAY DIFFRACTIONr_chiral_restr0.130.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214045
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 133 -
Rwork0.336 2953 -
obs--98.66 %

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