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- PDB-8ia6: Crystal structure of scFv antibody against Phospholipase A2 of Ec... -

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Basic information

Entry
Database: PDB / ID: 8ia6
TitleCrystal structure of scFv antibody against Phospholipase A2 of Echis carinatus venom
ComponentsscFv antibody
KeywordsIMMUNE SYSTEM / scFv / snake venom / Phospholipase A2 / Echis carinatus
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKumar, A. / Madni, Z.K. / Salunke, D.M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Mol.Immunol. / Year: 2024
Title: Recombinant human scFv antibody fragments against phospholipase A2 from Naja naja and Echis carinatus snake venoms: In vivo neutralization and mechanistic insights.
Authors: Kumar, A. / Madni, Z.K. / Chaturvedi, S. / Salunke, D.M.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scFv antibody
B: scFv antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,57611
Polymers53,7052
Non-polymers8719
Water2,972165
1
A: scFv antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4197
Polymers26,8531
Non-polymers5676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: scFv antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1574
Polymers26,8531
Non-polymers3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.890, 53.880, 169.326
Angle α, β, γ (deg.)90.000, 94.430, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Antibody scFv antibody


Mass: 26852.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M Citric acid, 0.05 M Bis-Tris propane pH 5.0, 16% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.75→33.35 Å / Num. obs: 15296 / % possible obs: 96.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 33.08 Å2 / CC1/2: 0.925 / Net I/σ(I): 4.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1580 / CC1/2: 0.613 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→29.23 Å / SU ML: 0.3316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 761 5.01 %
Rwork0.2323 14431 -
obs0.234 15192 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.08 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 57 165 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033498
X-RAY DIFFRACTIONf_angle_d0.61384734
X-RAY DIFFRACTIONf_chiral_restr0.0423520
X-RAY DIFFRACTIONf_plane_restr0.0047601
X-RAY DIFFRACTIONf_dihedral_angle_d5.7993508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.960.34231400.29122984X-RAY DIFFRACTION98.74
2.96-3.260.3371430.27042966X-RAY DIFFRACTION99.2
3.26-3.730.27531390.23462579X-RAY DIFFRACTION85.47
3.73-4.70.22611470.19682846X-RAY DIFFRACTION94.51
4.7-29.230.23731920.2213056X-RAY DIFFRACTION99.39

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