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- PDB-6my5: Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F... -

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Basic information

Entry
Database: PDB / ID: 6my5
TitleCrystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]
Components
  • anti-VEGF-A Fab fragment bH1 heavy chain
  • anti-VEGF-A Fab fragment bH1 light chain
KeywordsIMMUNE SYSTEM / Fab fragment / antibody assembly / dimeric Fab
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Epididymis luminal protein 214
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsShi, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)436202 Canada
CitationJournal: Mabs / Year: 2019
Title: Binding symmetry and surface flexibility mediate antibody self-association.
Authors: Schrag, J.D. / Picard, M.E. / Gaudreault, F. / Gagnon, L.P. / Baardsnes, J. / Manenda, M.S. / Sheff, J. / Deprez, C. / Baptista, C. / Hogues, H. / Kelly, J.F. / Purisima, E.O. / Shi, R. / Sulea, T.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: 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
H: anti-VEGF-A Fab fragment bH1 heavy chain
L: anti-VEGF-A Fab fragment bH1 light chain
A: anti-VEGF-A Fab fragment bH1 heavy chain
B: anti-VEGF-A Fab fragment bH1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1798
Polymers98,9304
Non-polymers2484
Water16,628923
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-57 kcal/mol
Surface area37060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.599, 65.530, 92.560
Angle α, β, γ (deg.)90.000, 100.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-VEGF-A Fab fragment bH1 heavy chain


Mass: 25438.496 Da / Num. of mol.: 2 / Mutation: Y33W,D98F,G99M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-3E7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: V9HW68
#2: Antibody anti-VEGF-A Fab fragment bH1 light chain


Mass: 24026.705 Da / Num. of mol.: 2 / Mutation: S30bR,S30bR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-3E7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q7Z3Y4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8 / Details: 0.04 M imidazole, pH 8.0, 21% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 100319 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.052 / Rrim(I) all: 0.107 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.73-1.764.10.58949660.7690.3330.678100
9.48-46.713.90.0636300.9920.0390.07596.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MXS

6mxs


Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.779 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.114
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4951 4.9 %RANDOM
Rwork0.1862 ---
obs0.1883 95349 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.72 Å2 / Biso mean: 23.583 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20.8 Å2
2--0.75 Å20 Å2
3----0.81 Å2
Refinement stepCycle: final / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 16 923 7661
Biso mean--32.44 32.69 -
Num. residues----879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026958
X-RAY DIFFRACTIONr_bond_other_d0.0010.026367
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9499482
X-RAY DIFFRACTIONr_angle_other_deg0.874314747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24723.852270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.615151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3431530
X-RAY DIFFRACTIONr_chiral_restr0.1160.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021585
LS refinement shellResolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 366 -
Rwork0.275 7115 -
all-7481 -
obs--100 %

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