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- PDB-8h73: Crystal structure of antibody scFv against M2e Influenza peptide -

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Basic information

Entry
Database: PDB / ID: 8h73
TitleCrystal structure of antibody scFv against M2e Influenza peptide
ComponentsSingle Chain Variable Fragment
KeywordsANTIVIRAL PROTEIN / scFv
Function / homologyCITRATE ANION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsKumar, U. / Madni, Z.K. / Gaur, V. / Salunke, D.M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: J.Biomed.Sci. / Year: 2023
Title: A structure and knowledge-based combinatorial approach to engineering universal scFv antibodies against influenza M2 protein.
Authors: Kumar, U. / Goyal, P. / Madni, Z.K. / Kamble, K. / Gaur, V. / Rajala, M.S. / Salunke, D.M.
History
DepositionOct 18, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Single Chain Variable Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9462
Polymers26,7571
Non-polymers1891
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-0 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.030, 175.030, 45.926
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Antibody Single Chain Variable Fragment


Mass: 26756.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.79 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4% MPD, 0.2M Citric acid pH 3.5, 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 31735 / % possible obs: 97.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 22.72 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.1
Reflection shellResolution: 1.91→1.98 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2923 / CC1/2: 0.694 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8H3B

8h3b


Resolution: 1.91→43.95 Å / SU ML: 0.1637 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.3251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2006 1581 4.98 %
Rwork0.1804 30153 -
obs0.1814 31734 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.66 Å2
Refinement stepCycle: LAST / Resolution: 1.91→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 13 181 1856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151720
X-RAY DIFFRACTIONf_angle_d1.08662334
X-RAY DIFFRACTIONf_chiral_restr0.0738255
X-RAY DIFFRACTIONf_plane_restr0.0082300
X-RAY DIFFRACTIONf_dihedral_angle_d7.1549249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.970.26661260.25262522X-RAY DIFFRACTION91.12
1.97-2.040.26131380.23542628X-RAY DIFFRACTION95.18
2.04-2.120.21961370.21132638X-RAY DIFFRACTION95.03
2.12-2.220.21721410.18382692X-RAY DIFFRACTION96.79
2.22-2.340.19731330.18032716X-RAY DIFFRACTION97.37
2.34-2.480.20051430.18532743X-RAY DIFFRACTION98.23
2.48-2.670.24461660.18442740X-RAY DIFFRACTION98.08
2.67-2.940.2211270.18072766X-RAY DIFFRACTION97.47
2.94-3.370.17761550.17232816X-RAY DIFFRACTION99.26
3.37-4.240.15831570.15152851X-RAY DIFFRACTION99.24
4.25-43.950.20281580.17813041X-RAY DIFFRACTION99.35

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