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- PDB-3wi4: Crystal structure of wild-type PorB from Neisseria meningitidis s... -

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Basic information

Entry
Database: PDB / ID: 3wi4
TitleCrystal structure of wild-type PorB from Neisseria meningitidis serogroup B
ComponentsMajor outer membrane protein P.IB
KeywordsMEMBRANE PROTEIN / beta-barrel / porin / outer membrane
Function / homology
Function and homology information


Toll Like Receptor TLR1:TLR2 Cascade / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / ER-Phagosome pathway
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Major outer membrane protein P.IB
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsKattner, C. / Toussi, D. / Wetzler, L.M. / Ruppel, N. / Massari, P. / Tanabe, M.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystallographic analysis of Neisseria meningitidis PorB extracellular loops potentially implicated in TLR2 recognition.
Authors: Kattner, C. / Toussi, D.N. / Zaucha, J. / Wetzler, L.M. / Ruppel, N. / Zachariae, U. / Massari, P. / Tanabe, M.
History
DepositionSep 5, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major outer membrane protein P.IB


Theoretical massNumber of molelcules
Total (without water)33,9581
Polymers33,9581
Non-polymers00
Water0
1
A: Major outer membrane protein P.IB

A: Major outer membrane protein P.IB

A: Major outer membrane protein P.IB


Theoretical massNumber of molelcules
Total (without water)101,8753
Polymers101,8753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6890 Å2
ΔGint-63 kcal/mol
Surface area42320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.291, 148.291, 104.045
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Major outer membrane protein P.IB / PIB / Protein IB / Class 3 protein / Porin


Mass: 33958.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: porB, NMB2039 / Production host: Escherichia coli (E. coli) / References: UniProt: P30690

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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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MES pH 6.5-7.0, 50mM CsCl, 35% (v/v) Jeffamine M-600, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2013
RadiationMonochromator: toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→80.84 Å / Num. all: 17921 / Num. obs: 6628 / % possible obs: 92.8 % / Observed criterion σ(F): 9.5 / Observed criterion σ(I): 3.5
Reflection shellResolution: 3.3→3.37 Å / % possible all: 76.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→50 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.844 / Cross valid method: THROUGHOUT / ESU R Free: 0.745 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29352 535 9.8 %RANDOM
Rwork0.25399 ---
obs0.2579 4948 50 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.657 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 3.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 0 0 2372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9223281
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8124.553123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.89915386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.3551513
X-RAY DIFFRACTIONr_chiral_restr0.1090.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021902
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: 3.319→3.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 28 -
Rwork0.26 233 -
obs--55.06 %

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