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

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Basic information

Entry
Database: PDB / ID: 7lcv
TitleFactor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein
Components
  • Factor H binding protein
  • Immunoglobulin heavy chain Fd fragment
  • Immunoglobulin kappa light chain
KeywordsIMMUNE SYSTEM / human / antibody / Fab / meningococcal vaccine / Factor H binding protein / complex
Function / homology: / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-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: 1.7 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
DepositionJan 11, 2021Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,6895
Polymers75,6183
Non-polymers712
Water5,423301
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)39.470, 52.370, 84.560
Angle α, β, γ (deg.)73.781, 84.482, 74.173
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody Immunoglobulin heavy chain Fd fragment


Mass: 23978.697 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 kappa light chain


Mass: 23565.068 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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M LiNO3, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.7→81.18 Å / Num. obs: 65915 / % possible obs: 93.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.68 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 11.59
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6477 / CC1/2: 0.798 / CC star: 0.942 / Rpim(I) all: 0.513 / Rrim(I) all: 0.983 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CVD and Fab homology model

3cvd


Resolution: 1.7→81.18 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.8457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2697 1120 1.75 %
Rwork0.2395 62991 -
obs0.2401 64111 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.72 Å2
Refinement stepCycle: LAST / Resolution: 1.7→81.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 2 301 5026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01724819
X-RAY DIFFRACTIONf_angle_d2.02416522
X-RAY DIFFRACTIONf_chiral_restr0.1059729
X-RAY DIFFRACTIONf_plane_restr0.0099846
X-RAY DIFFRACTIONf_dihedral_angle_d17.39981733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.780.34051360.35287905X-RAY DIFFRACTION93.39
1.78-1.870.37971470.32827938X-RAY DIFFRACTION93.27
1.87-1.990.44411390.38347735X-RAY DIFFRACTION92.12
1.99-2.140.35621380.28637988X-RAY DIFFRACTION94.81
2.14-2.360.36381470.337878X-RAY DIFFRACTION92.87
2.36-2.70.33991460.27868028X-RAY DIFFRACTION95.08
2.7-3.40.23291290.24197729X-RAY DIFFRACTION91.47
3.4-81.180.21151380.17937790X-RAY DIFFRACTION92

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