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- PDB-8rtw: Crystal Structure of the Anti-testosterone Fab in Complex with Te... -

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Basic information

Entry
Database: PDB / ID: 8rtw
TitleCrystal Structure of the Anti-testosterone Fab in Complex with Testosterone
Components
  • Anti-testosterone Fab 220 heavy chain
  • Anti-testosterone Fab 220 light chain
KeywordsIMMUNE SYSTEM / Fab / Testosterone
Function / homologyTESTOSTERONE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsEronen, V. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Febs J. / Year: 2024
Title: Structural insights into ternary immunocomplex formation and cross-reactivity: binding of an anti-immunocomplex FabB12 to Fab220-testosterone complex.
Authors: Eronen, V. / Takkinen, K. / Torni, A. / Peng, K. / Janis, J. / Parkkinen, T. / Hakulinen, N. / Rouvinen, J.
History
DepositionJan 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-testosterone Fab 220 light chain
B: Anti-testosterone Fab 220 heavy chain
C: Anti-testosterone Fab 220 light chain
D: Anti-testosterone Fab 220 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8176
Polymers97,2404
Non-polymers5772
Water7,206400
1
A: Anti-testosterone Fab 220 light chain
B: Anti-testosterone Fab 220 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9083
Polymers48,6202
Non-polymers2881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-31 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: Anti-testosterone Fab 220 light chain
D: Anti-testosterone Fab 220 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9083
Polymers48,6202
Non-polymers2881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-30 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.376, 53.159, 111.947
Angle α, β, γ (deg.)90.000, 96.400, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Anti-testosterone Fab 220 light chain


Mass: 23938.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Anti-testosterone Fab 220 heavy chain


Mass: 24681.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium sulfate, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.99→48.02 Å / Num. obs: 60707 / % possible obs: 95.43 % / Redundancy: 2.67 % / Biso Wilson estimate: 43.1 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.65
Reflection shellResolution: 1.99→2.05 Å / Num. unique obs: 5889 / CC1/2: 0.459

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.02 Å / SU ML: 0.3105 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1161
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 1998 3.29 %
Rwork0.1895 58676 -
obs0.1905 60674 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.08 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 42 400 7078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886858
X-RAY DIFFRACTIONf_angle_d1.10049358
X-RAY DIFFRACTIONf_chiral_restr0.06591044
X-RAY DIFFRACTIONf_plane_restr0.01111186
X-RAY DIFFRACTIONf_dihedral_angle_d16.85182432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.37421390.3434072X-RAY DIFFRACTION92.88
2.04-2.10.3161390.31734108X-RAY DIFFRACTION95.1
2.1-2.160.30511450.29364247X-RAY DIFFRACTION97.71
2.16-2.230.3091440.25814247X-RAY DIFFRACTION97.04
2.23-2.310.32261450.24494252X-RAY DIFFRACTION97.15
2.31-2.40.31361440.23474247X-RAY DIFFRACTION97.69
2.4-2.510.28521430.22934187X-RAY DIFFRACTION96.05
2.51-2.650.2641450.22134248X-RAY DIFFRACTION96.59
2.65-2.810.26551430.21584215X-RAY DIFFRACTION95.78
2.81-3.030.24921440.1974208X-RAY DIFFRACTION96.5
3.03-3.330.20631410.19514157X-RAY DIFFRACTION94.54
3.33-3.810.211420.16854164X-RAY DIFFRACTION94.33
3.81-4.80.17891420.14514153X-RAY DIFFRACTION93.7
4.81-48.020.1621420.16044171X-RAY DIFFRACTION91.42

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