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- PDB-7ke1: Factor H enhancing human antibody fragment (Fab) to meningococcal... -

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Basic information

Entry
Database: PDB / ID: 7ke1
TitleFactor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein
Components(Immunoglobulin gamma, ...) x 2
KeywordsIMMUNE SYSTEM / human / antibody / Fab / meningococcal vaccine / Factor H binding protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 9, 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 1.2Apr 3, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Immunoglobulin gamma, kappa light chain
A: Immunoglobulin gamma, heavy chain Fd fragment
D: Immunoglobulin gamma, kappa light chain
C: Immunoglobulin gamma, heavy chain Fd fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,25315
Polymers97,5094
Non-polymers74511
Water16,177898
1
B: Immunoglobulin gamma, kappa light chain
A: Immunoglobulin gamma, heavy chain Fd fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,30010
Polymers48,7542
Non-polymers5468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-74 kcal/mol
Surface area19560 Å2
MethodPISA
2
D: Immunoglobulin gamma, kappa light chain
C: Immunoglobulin gamma, heavy chain Fd fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9535
Polymers48,7542
Non-polymers1993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-68 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.771, 97.260, 70.472
Angle α, β, γ (deg.)90.000, 90.373, 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

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Antibody , 2 types, 4 molecules BDAC

#1: Antibody Immunoglobulin gamma, kappa light chain


Mass: 23661.219 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 5 types, 909 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Bis-Tris Propane, lithium sulfate

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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: 1.5→70.47 Å / Num. obs: 143102 / % possible obs: 98.07 % / Observed criterion σ(I): 1.89 / Redundancy: 6.9 % / Biso Wilson estimate: 18.13 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1672 / Rpim(I) all: 0.067 / Rrim(I) all: 0.18 / Net I/σ(I): 12.18
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 7 % / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 97061 / CC1/2: 0.702 / Rpim(I) all: 0.394 / Rrim(I) all: 1.086 / % possible all: 96.35

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Processing

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

Resolution: 1.5→70.47 Å / SU ML: 0.1631 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1826 1441 1.01 %
Rwork0.1621 141476 -
obs0.1623 142917 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→70.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 39 898 7455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01126907
X-RAY DIFFRACTIONf_angle_d1.26469470
X-RAY DIFFRACTIONf_chiral_restr0.07061084
X-RAY DIFFRACTIONf_plane_restr0.00891213
X-RAY DIFFRACTIONf_dihedral_angle_d16.72322550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.26021400.237313782X-RAY DIFFRACTION96.35
1.55-1.620.28911420.215713949X-RAY DIFFRACTION96.85
1.62-1.690.24531430.196913973X-RAY DIFFRACTION97.13
1.69-1.780.21411420.178314044X-RAY DIFFRACTION97.6
1.78-1.890.19421450.164114118X-RAY DIFFRACTION97.93
1.89-2.040.18821440.155814169X-RAY DIFFRACTION98.31
2.04-2.240.1691450.151914205X-RAY DIFFRACTION98.69
2.24-2.560.19921450.160814346X-RAY DIFFRACTION99.19
2.56-3.230.20861470.168314395X-RAY DIFFRACTION99.34
3.23-70.470.13941480.146314495X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: -14.6945270849 Å / Origin y: -16.2579363628 Å / Origin z: -6.11518543547 Å
111213212223313233
T0.130943158807 Å20.00564968535414 Å20.00637587991276 Å2-0.126140068866 Å20.00173616308514 Å2--0.13468301567 Å2
L0.11081432432 °20.0125732204667 °20.0974341509351 °2-0.0368550462249 °2-0.0100072498539 °2--0.153882094788 °2
S0.00071712853399 Å °-0.00136829947367 Å °-0.000770287166659 Å °0.00189554622332 Å °0.000388049367548 Å °0.00166704329941 Å °-5.9656917244E-5 Å °-0.0287945072058 Å °1.29876976497E-11 Å °
Refinement TLS groupSelection details: all

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