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- PDB-8r3w: Crystal structure of a homospecific CR57 diabody -

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Basic information

Entry
Database: PDB / ID: 8r3w
TitleCrystal structure of a homospecific CR57 diabody
ComponentsHomospecific Diabody CR57
KeywordsIMMUNE SYSTEM / human monoclonal antibody CR57 / diabody / monospecific diabody / rabies antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsKedari, A. / Rissanen, I.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland#342988, # 346508 Finland
University of Helsinki Finland
Finnish Cultural Foundation#00240631 Finland
CitationJournal: Structure / Year: 2024
Title: Structural insight into rabies virus neutralization revealed by an engineered antibody scaffold.
Authors: Kedari, A. / Iheozor-Ejiofor, R. / Salminen, P. / Ugurlu, H. / Makela, A.R. / Levanov, L. / Vapalahti, O. / Hytonen, V.P. / Saksela, K. / Rissanen, I.
History
DepositionNov 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2Dec 18, 2024Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homospecific Diabody CR57
R: Homospecific Diabody CR57


Theoretical massNumber of molelcules
Total (without water)56,1162
Polymers56,1162
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Elutes as a dimer from size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-25 kcal/mol
Surface area21380 Å2
Unit cell
Length a, b, c (Å)64.780, 65.000, 122.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Homospecific Diabody CR57


Mass: 28057.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: Trapezoidal prism
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M magnesium chloride, 0.1M bis-Tris pH 5.5, 25% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.38→57.24 Å / Num. obs: 21408 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.068 / Net I/σ(I): 9.5
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.344 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1066 / CC1/2: 0.492 / Rpim(I) all: 0.498

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Processing

Software
NameVersionClassification
PHENIX1.19rc6-4061refinement
xia23.10.0data scaling
xia23.10.0data reduction
PHENIX1.19rc6-4061phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→44.53 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1009 4.72 %
Rwork0.1907 --
obs0.1925 21356 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 0 67 3668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023689
X-RAY DIFFRACTIONf_angle_d0.5025014
X-RAY DIFFRACTIONf_dihedral_angle_d4.342523
X-RAY DIFFRACTIONf_chiral_restr0.045537
X-RAY DIFFRACTIONf_plane_restr0.004652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.510.3481420.28232867X-RAY DIFFRACTION100
2.51-2.660.32771250.25252869X-RAY DIFFRACTION100
2.66-2.870.28511480.24272857X-RAY DIFFRACTION100
2.87-3.160.27921400.20972888X-RAY DIFFRACTION100
3.16-3.610.22871460.19612888X-RAY DIFFRACTION100
3.61-4.550.22211550.16492909X-RAY DIFFRACTION100
4.55-44.530.17321530.16643069X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1362.0798-0.39253.03880.0147.4186-0.0441-0.1789-0.32170.11160.0768-0.11840.42680.123-0.06170.32910.03450.02380.23120.03960.5322.5096-53.532255.3764
21.7982-0.38741.634.8018-1.00335.11180.0183-0.05180.0457-0.0728-0.0844-0.0891-0.0998-0.31680.07560.27860.01870.02150.2377-0.01330.395814.6689-43.345319.9826
35.7567-1.40441.15934.5233-0.38346.8120.0541-0.42670.26540.263-0.04720.1451-0.698-0.5222-0.01740.47970.11420.00080.4347-0.08510.48328.4982-26.756331.0027
43.1171.0653-0.07634.55-1.57016.1917-0.065-0.09710.06220.2537-0.01130.168-0.0383-0.42360.09670.29230.00530.0340.25570.00520.413932.4383-34.622154.0781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 120 )
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 240 )
3X-RAY DIFFRACTION3chain 'R' and (resid 2 through 125 )
4X-RAY DIFFRACTION4chain 'R' and (resid 126 through 240 )

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