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- PDB-5t5f: Neisseria meningitidis factor H binding protein in complex with m... -

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Basic information

Entry
Database: PDB / ID: 5t5f
TitleNeisseria meningitidis factor H binding protein in complex with monoclonal antibody JAR5
Components
  • Factor H binding protein variant B24
  • Monoclonal antibody Jar5 heavy chain
  • Monoclonal antibody Jar5 light chain
KeywordsPROTEIN BINDING / fHbp / JAR5 / epitope mapping / monoclonal antibody / cooperativity / Neisseria meningitidis
Function / homology
Function and homology information


bacterial extracellular vesicle / cell outer membrane
Similarity search - Function
Immunoglobulin-like - #1980 / : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Immunoglobulin-like - #1980 / : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Factor H binding protein variant B24 / Factor H binding protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsMalito, E.
CitationJournal: Biochem. J. / Year: 2016
Title: Neisseria meningitidis factor H-binding protein bound to monoclonal antibody JAR5: implications for antibody synergy.
Authors: Malito, E. / Lo Surdo, P. / Veggi, D. / Santini, L. / Stefek, H. / Brunelli, B. / Luzzi, E. / Bottomley, M.J. / Beernink, P.T. / Scarselli, M.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Factor H binding protein variant B24
H: Monoclonal antibody Jar5 heavy chain
L: Monoclonal antibody Jar5 light chain


Theoretical massNumber of molelcules
Total (without water)73,9093
Polymers73,9093
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-28 kcal/mol
Surface area28830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.370, 146.490, 218.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Factor H binding protein variant B24 / Factor H binding protein variant B24_001 / Factor H binding protein variant B24_002 / Factor H ...Factor H binding protein variant B24_001 / Factor H binding protein variant B24_002 / Factor H binding protein variant B24_004 / Factor H binding protein variant B24_005 / Factor H binding protein variant B24_006 / Factor H binding protein variant B24_007 / Factor H binding protein variant B24_008 / Factor H binding protein variant B24_010 / Putative lipoprotein


Mass: 26838.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: fhbp
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6VRZ6, UniProt: Q9JXV4*PLUS
#2: Antibody Monoclonal antibody Jar5 heavy chain


Mass: 23204.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Monoclonal antibody Jar5 light chain


Mass: 23865.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.57 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% Polyethylene glycol (PEG) 6000 0.1 M tri-Sodium citrate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→73.24 Å / Num. obs: 21885 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 84.05 Å2 / CC1/2: 0.97 / Rsym value: 0.2 / Net I/σ(I): 5.5
Reflection shellResolution: 2.98→3.16 Å / Redundancy: 5 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3437 / CC1/2: 0.429 / Rsym value: 1.096 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W80

2w80


Resolution: 2.98→59.7 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.839 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.113 / SU Rfree Blow DPI: 0.383 / SU Rfree Cruickshank DPI: 0.391
Details: The target-structure restraints option (LSSR) was used while refining in BUSTER, using as fixed coordinates those of fHbp (chain A of this entry) from PDB 2YPV.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1047 4.79 %RANDOM
Rwork0.223 ---
obs0.225 21848 99.9 %-
Displacement parametersBiso mean: 69.63 Å2
Baniso -1Baniso -2Baniso -3
1--7.1114 Å20 Å20 Å2
2---3.9501 Å20 Å2
3---11.0615 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: 1 / Resolution: 2.98→59.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5023 0 0 34 5057
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015138HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.236964HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2341SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes749HARMONIC5
X-RAY DIFFRACTIONt_it5138HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion3.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion676SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5642SEMIHARMONIC4
LS refinement shellResolution: 2.98→3.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.289 126 4.43 %
Rwork0.248 2717 -
all0.25 2843 -
obs--99.54 %

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