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- PDB-7ket: Factor H enhancing human antibody fragment (Fab) to meningococcal... -

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Basic information

Entry
Database: PDB / ID: 7ket
TitleFactor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein
Components
  • Factor H binding protein
  • Immunoglobulin gamma, heavy chain Fd fragment
  • Immunoglobulin gamma, kappa light chain
KeywordsIMMUNE SYSTEM / human / antibody / Fab / meningococcal vaccine / Factor H binding protein / complex
Function / homologyFactor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Factor H binding protein variant B24
Function and homology information
Biological speciesHomo sapiens (human)
Neisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBeernink, P.T. / Sands, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI134868 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site.
Authors: Sands, N.A. / Beernink, P.T.
History
DepositionOct 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Immunoglobulin gamma, kappa light chain
A: Immunoglobulin gamma, heavy chain Fd fragment
C: Factor H binding protein


Theoretical massNumber of molelcules
Total (without water)76,8293
Polymers76,8293
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.580, 86.030, 107.890
Angle α, β, γ (deg.)90.000, 96.907, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Immunoglobulin gamma, kappa light chain


Mass: 23661.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Immunoglobulin gamma, heavy chain Fd fragment


Mass: 25093.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Factor H binding protein


Mass: 28074.248 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 (E. coli) / References: UniProt: Q6VRZ6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, polyethylene glycol 3350, tryptone, sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 6, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2→107.11 Å / Num. obs: 46166 / % possible obs: 94.96 % / Redundancy: 2.7 % / Biso Wilson estimate: 45.33 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.071 / Rrim(I) all: 0.123 / Net I/σ(I): 8.02
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.66 / Num. unique obs: 3877 / Rpim(I) all: 1.24 / Rrim(I) all: 2.09 / % possible all: 82.44

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Processing

Software
NameVersionClassification
Coot1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model constructed from human Fab; FHbp ID 1 (3KVD)

3kvd


Resolution: 2→107.11 Å / SU ML: 0.4524 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 40.2514
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2814 1571 3.49 %
Rwork0.234 43400 -
obs0.2356 44971 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.91 Å2
Refinement stepCycle: LAST / Resolution: 2→107.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5057 0 0 162 5219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085189
X-RAY DIFFRACTIONf_angle_d1.12117028
X-RAY DIFFRACTIONf_chiral_restr0.072789
X-RAY DIFFRACTIONf_plane_restr0.0079911
X-RAY DIFFRACTIONf_dihedral_angle_d19.74651907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.45061390.4013382X-RAY DIFFRACTION82.23
2.06-2.140.38791310.383834X-RAY DIFFRACTION91.91
2.14-2.220.39561440.3783899X-RAY DIFFRACTION95.06
2.22-2.330.48631400.43033670X-RAY DIFFRACTION88.91
2.33-2.450.41971460.33294092X-RAY DIFFRACTION98.47
2.45-2.60.38561400.31634115X-RAY DIFFRACTION98.88
2.6-2.80.33951460.28364053X-RAY DIFFRACTION98.27
2.8-3.080.32981430.27184105X-RAY DIFFRACTION98.77
3.08-3.530.32271500.23154093X-RAY DIFFRACTION98.1
3.53-4.450.2431510.19064044X-RAY DIFFRACTION96.99
4.45-107.110.18831410.16874113X-RAY DIFFRACTION96.88
Refinement TLS params.Method: refined / Origin x: -16.2387422764 Å / Origin y: 18.14211792 Å / Origin z: -18.5711456552 Å
111213212223313233
T0.383228635159 Å20.017125991141 Å20.0736806673347 Å2-0.243557630418 Å2-0.0156309302341 Å2--0.379796900502 Å2
L1.2371820073 °2-0.364001487308 °21.96473768932 °2-0.354471826814 °2-0.801857374661 °2--4.0592785871 °2
S0.0908274206607 Å °-0.0430480432294 Å °-0.0617268915422 Å °0.0772860286701 Å °-0.00381640954862 Å °-0.0243778605434 Å °0.153512154041 Å °-0.0968194376871 Å °-0.0856052631099 Å °
Refinement TLS groupSelection details: all

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