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- PDB-7ah1: L19 diabody fragment from immunocytokine L19-IL2 -

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Basic information

Entry
Database: PDB / ID: 7ah1
TitleL19 diabody fragment from immunocytokine L19-IL2
ComponentsAnti-(ED-B) scFV
KeywordsIMMUNE SYSTEM / immunocytokine / protein engineering / cancer therapeutics
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOngaro, T. / Guarino, S.R. / Scietti, L. / Palamini, M. / Wulhfard, S. / Villa, A. / Neri, D. / Forneris, F.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 20075 Italy
Italian Ministry of EducationDipartimenti di Eccellenza 2018-2022 Italy
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Inference of molecular structure for characterization and improvement of clinical grade immunocytokines.
Authors: Ongaro, T. / Guarino, S.R. / Scietti, L. / Palamini, M. / Wulhfard, S. / Neri, D. / Villa, A. / Forneris, F.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-(ED-B) scFV


Theoretical massNumber of molelcules
Total (without water)26,1411
Polymers26,1411
Non-polymers00
Water3,981221
1
A: Anti-(ED-B) scFV

A: Anti-(ED-B) scFV


Theoretical massNumber of molelcules
Total (without water)52,2822
Polymers52,2822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3580 Å2
ΔGint-22 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.810, 91.138, 99.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

21A-518-

HOH

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Components

#1: Antibody Anti-(ED-B) scFV


Mass: 26140.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-S / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A2KBC1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 10 mg/ml in 100 mM HEPES/NaOH, 10% PEG 6000, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.5 Å / Num. obs: 17195 / % possible obs: 99.7 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.1 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.163 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1241 / CC1/2: 0.705 / Rpim(I) all: 0.827 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS1

5gs1


Resolution: 2→41.45 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2204 -5 %
Rwork0.198 --
obs-17178 99.32 %
Displacement parametersBiso mean: 33.43 Å2
Refinement stepCycle: LAST / Resolution: 2→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 0 221 1946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381791
X-RAY DIFFRACTIONf_angle_d0.76682437
X-RAY DIFFRACTIONf_chiral_restr0.0484265
X-RAY DIFFRACTIONf_plane_restr0.0039315
X-RAY DIFFRACTIONf_dihedral_angle_d13.0211070
LS refinement shellResolution: 2→2.072 Å
RfactorNum. reflection% reflection
Rfree0.3895 -5 %
Rwork0.3081 3333 -
obs--99.11 %

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