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- PDB-8h3b: Crystal structure of antibody scFv against M2e Influenza peptide -

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Basic information

Entry
Database: PDB / ID: 8h3b
TitleCrystal structure of antibody scFv against M2e Influenza peptide
ComponentsSingle Chain Variable Fragment
KeywordsANTIVIRAL PROTEIN / Single chain variable fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 8, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
A: Single Chain Variable Fragment
B: Single Chain Variable Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3503
Polymers54,2582
Non-polymers921
Water1,29772
1
A: Single Chain Variable Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2212
Polymers27,1291
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Single Chain Variable Fragment


Theoretical massNumber of molelcules
Total (without water)27,1291
Polymers27,1291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.973, 106.973, 149.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 4 or (resid 5...
d_2ens_1(chain "B" and (resid 3 through 77 or (resid 78...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 3 - 241 / Label seq-ID: 3 - 241

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999509173016, 0.0237495284529, 0.0204297076704), (-0.00856401377243, -0.834434178636, 0.551041068517), (0.0301342118752, 0.550595642394, 0.834228007113)Vector: 44. ...NCS oper: (Code: given
Matrix: (-0.999509173016, 0.0237495284529, 0.0204297076704), (-0.00856401377243, -0.834434178636, 0.551041068517), (0.0301342118752, 0.550595642394, 0.834228007113)
Vector: 44.7440644248, 28.4638386213, -9.20660067521)

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Components

#1: Antibody Single Chain Variable Fragment


Mass: 27129.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 4M Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.75→75.64 Å / Num. obs: 23027 / % possible obs: 99.6 % / Redundancy: 10 % / Biso Wilson estimate: 52.72 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.9
Reflection shellResolution: 2.75→2.8 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1110 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
PHENIXdev_4753refinement
PHENIXdev_4753refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DSI

6dsi


Resolution: 2.75→75.64 Å / SU ML: 0.2696 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2148 1139 4.95 %
Rwork0.1808 21884 -
obs0.1779 23023 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.46 Å2
Refinement stepCycle: LAST / Resolution: 2.75→75.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 6 72 3482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263481
X-RAY DIFFRACTIONf_angle_d0.66214721
X-RAY DIFFRACTIONf_chiral_restr0.0443526
X-RAY DIFFRACTIONf_plane_restr0.0049602
X-RAY DIFFRACTIONf_dihedral_angle_d15.59011238
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.558538674498 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.880.30731330.25152670X-RAY DIFFRACTION99.4
2.88-3.030.29611430.23572686X-RAY DIFFRACTION100
3.03-3.220.26821660.21922683X-RAY DIFFRACTION99.96
3.22-3.470.22711420.1912691X-RAY DIFFRACTION99.72
3.47-3.820.19021430.17072716X-RAY DIFFRACTION99.76
3.82-4.370.19321420.14532726X-RAY DIFFRACTION99.83
4.37-5.510.14451360.13242782X-RAY DIFFRACTION99.59
5.51-75.640.18991340.19252930X-RAY DIFFRACTION98.77

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