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- PDB-6n7u: apo-BDBV223 Fab -

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Basic information

Entry
Database: PDB / ID: 6n7u
Titleapo-BDBV223 Fab
Components
  • BDBV223 antibody heavy chain
  • BDBV223 antibody light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / antiviral protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKing, L.B. / West, B.R. / Saphire, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 109762 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109711 United States
CitationJournal: Nat Commun / Year: 2019
Title: Cross-reactive neutralizing human survivor monoclonal antibody BDBV223 targets the ebolavirus stalk.
Authors: King, L.B. / West, B.R. / Moyer, C.L. / Gilchuk, P. / Flyak, A. / Ilinykh, P.A. / Bombardi, R. / Hui, S. / Huang, K. / Bukreyev, A. / Crowe Jr., J.E. / Saphire, E.O.
History
DepositionNov 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / 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
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: BDBV223 antibody heavy chain
B: BDBV223 antibody light chain


Theoretical massNumber of molelcules
Total (without water)48,4002
Polymers48,4002
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-24 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.975, 75.678, 114.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody BDBV223 antibody heavy chain


Mass: 24582.586 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody BDBV223 antibody light chain


Mass: 23817.580 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 80 mM sodium citrate tribasic/hydrochloric acid, pH 5.6, 20% PEG300, 200 mM ammonium sulfate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 2.03→45.63 Å / Num. obs: 37109 / % possible obs: 99.82 % / Redundancy: 6.1 % / CC1/2: 0.95 / Net I/σ(I): 12.6
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.6 / CC1/2: 0.85 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6N7J

6n7j


Resolution: 2.03→45.63 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.05
RfactorNum. reflection% reflection
Rfree0.2497 1895 5.11 %
Rwork0.2346 --
obs0.2354 37105 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.03→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 164 3324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033235
X-RAY DIFFRACTIONf_angle_d0.714394
X-RAY DIFFRACTIONf_dihedral_angle_d10.9131155
X-RAY DIFFRACTIONf_chiral_restr0.026498
X-RAY DIFFRACTIONf_plane_restr0.004561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.08080.29271240.28242477X-RAY DIFFRACTION100
2.0808-2.13710.30681350.28752456X-RAY DIFFRACTION100
2.1371-2.20.28631240.27292494X-RAY DIFFRACTION100
2.2-2.2710.33021280.27512496X-RAY DIFFRACTION100
2.271-2.35210.32371150.27752504X-RAY DIFFRACTION100
2.3521-2.44630.28461410.28162488X-RAY DIFFRACTION100
2.4463-2.55760.30711320.2912486X-RAY DIFFRACTION100
2.5576-2.69240.30261370.29612510X-RAY DIFFRACTION100
2.6924-2.86110.28771270.27862527X-RAY DIFFRACTION100
2.8611-3.0820.27031320.27872508X-RAY DIFFRACTION100
3.082-3.3920.27651660.26232493X-RAY DIFFRACTION100
3.392-3.88260.23021480.23142530X-RAY DIFFRACTION100
3.8826-4.89080.20091430.18792551X-RAY DIFFRACTION99
4.8908-45.64620.23371430.20412690X-RAY DIFFRACTION100

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