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

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Basic information

Entry
Database: PDB / ID: 6mxs
TitleCrystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
Components(anti-VEGF-A Fab fragment bH1 ...) x 2
KeywordsIMMUNE SYSTEM / Fab fragment / antibody assembly / aggregation
Function / homology
Function and homology information


extracellular region / 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: 1.95 Å
AuthorsShi, R. / Picard, M.-E. / Manenda, M.S.
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
DepositionOct 31, 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 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)99,0089
Polymers98,7904
Non-polymers2185
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, DLS and ITC data also support the dimeric assembly of Fab variant
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-89 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.679, 95.960, 110.110
Angle α, β, γ (deg.)90.000, 103.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#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: 23956.588 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 849 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.6
Details: 0.1 M tri-sodium citrate, pH 5.6, 12% PEG4000, 10% isopropanol

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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 7, 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: 1.95→50 Å / Num. obs: 95751 / % possible obs: 99.1 % / Redundancy: 3.7 % / CC1/2: 0.947 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.134 / Rrim(I) all: 0.261 / Net I/σ(I): 26.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-1.983.80.89347150.5370.5331.04298.4
10.68-49.863.60.1496080.9260.0890.17498.3

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BDY

3bdy


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.884 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.132
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 4831 5.1 %RANDOM
Rwork0.1913 ---
obs0.1932 90638 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.79 Å2 / Biso mean: 29.286 Å2 / Biso min: 12.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å2-0 Å2-0.78 Å2
2---0.94 Å20 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 11 844 7504
Biso mean--37.91 37.73 -
Num. residues----870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.026891
X-RAY DIFFRACTIONr_bond_other_d0.0010.026280
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9499395
X-RAY DIFFRACTIONr_angle_other_deg0.882314542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5365.011883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05723.978269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.064151077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.811528
X-RAY DIFFRACTIONr_chiral_restr0.1150.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021572
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 340 -
Rwork0.336 6654 -
all-6994 -
obs--97.48 %

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