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- PDB-9hy3: sc-4E (scFv derived from the mAb 4E1 against CD93) crystallized a... -

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Basic information

Entry
Database: PDB / ID: 9hy3
Titlesc-4E (scFv derived from the mAb 4E1 against CD93) crystallized at pH 5.5
Componentssc-4E (scFv derived from the mAb 4E1 against CD93)
KeywordsIMMUNE SYSTEM / single-chain antibody fragment / scFv / monoclonal antibody 4E1 against CD93 / sc-4E
Function / homologyIMIDAZOLE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsRaucci, L. / Orlandini, M. / Pozzi, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)BC63C22000680007European Union
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural and antigen-binding surface definition of an anti-CD93 monoclonal antibody for the treatment of degenerative vascular eye diseases.
Authors: Raucci, L. / Perrone, C.D. / Barbera, S. / de Boer, L.J. / Tosi, G.M. / Brunetti, J. / Bracci, L. / Pozzi, C. / Galvagni, F. / Orlandini, M.
History
DepositionJan 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sc-4E (scFv derived from the mAb 4E1 against CD93)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,29611
Polymers28,8521
Non-polymers44310
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric state sample in solution (obtained from gel filtration)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-37 kcal/mol
Surface area11110 Å2
Unit cell
Length a, b, c (Å)64.531, 64.531, 160.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

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Antibody , 1 types, 1 molecules A

#1: Antibody sc-4E (scFv derived from the mAb 4E1 against CD93)


Mass: 28852.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS

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Non-polymers , 5 types, 344 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 4.3 M NaCl, 0.1 M bis-tris pH 5.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.62→52.78 Å / Num. obs: 49253 / % possible obs: 98.1 % / Redundancy: 8.8 % / Biso Wilson estimate: 30.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.026 / Rrim(I) all: 0.078 / Χ2: 1.07 / Net I/σ(I): 13.5
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 9 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2457 / CC1/2: 0.584 / Rpim(I) all: 0.344 / Rrim(I) all: 1.041 / Χ2: 0.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→52.78 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.812 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20673 2461 5.1 %RANDOM
Rwork0.17534 ---
obs0.17687 46242 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.658 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.62→52.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 23 334 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.8022532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1275242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.96257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01510281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1530.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021463
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2972.213941
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1413.951177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5442.45929
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.08328.222893
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 201 -
Rwork0.432 3443 -
obs--99.21 %
Refinement TLS params.Method: refined / Origin x: -32.0052 Å / Origin y: 6.2983 Å / Origin z: 9.7419 Å
111213212223313233
T0.1432 Å2-0.0458 Å2-0.0475 Å2-0.0584 Å20.0309 Å2--0.087 Å2
L0.122 °2-0.0288 °2-0.0145 °2-0.3886 °20.0343 °2--0.5324 °2
S-0.0233 Å °0.0157 Å °-0.0453 Å °0.0225 Å °0.121 Å °0.0512 Å °-0.0717 Å °0.0233 Å °-0.0977 Å °

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