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- PDB-1l7t: Crystal Structure Analysis of the anti-testosterone Fab fragment -

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Basic information

Entry
Database: PDB / ID: 1l7t
TitleCrystal Structure Analysis of the anti-testosterone Fab fragment
Components
  • anti-testosterone (heavy chain)
  • anti-testosterone (light chain)
KeywordsIMMUNE SYSTEM / anti-testosterone / fab fragment / affinity and specificity matured
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / adaptive immune response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig gamma-1 chain C region, membrane-bound form / Kappa light chain C_region / Ighg protein / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsValjakka, J. / Hemminki, A. / Niemi, S. / Soderlund, H. / Takkinen, K. / Rouvinen, J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of an in Vitro Affinity- and Specificity-matured Anti-testosterone Fab in Complex with Testosterone. IMPROVED AFFINITY RESULTS FROM SMALL STRUCTURAL CHANGES WITHIN THE VARIABLE DOMAINS
Authors: Valjakka, J. / Hemminki, A. / Niemi, S. / Soderlund, H. / Takkinen, K. / Rouvinen, J.
History
DepositionMar 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence an appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: anti-testosterone (light chain)
H: anti-testosterone (heavy chain)


Theoretical massNumber of molelcules
Total (without water)47,7362
Polymers47,7362
Non-polymers00
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-24 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.695, 88.419, 143.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody anti-testosterone (light chain)


Mass: 24151.910 Da / Num. of mol.: 1 / Fragment: fab77 fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKKtac / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: Q99M37, UniProt: Q65ZC0*PLUS
#2: Antibody anti-testosterone (heavy chain)


Mass: 23583.697 Da / Num. of mol.: 1 / Fragment: fab77 fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKKtac / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: P01869, UniProt: Q91Z05*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: peg3350, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.6 / Details: Valjakka, J., (2002) J.Biol.Chem., 277, 4183.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
20.1 MBis-Tris propane1droppH5.6
315 %PEG33501drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 23, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 22855 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.1→2.18 Å / % possible all: 87.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 500 Å / Num. obs: 25386 / Num. measured all: 120393 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 87.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å
RfactorNum. reflectionSelection details
Rfree0.275 20521 random
Rwork0.213 --
all-27083 -
obs-22855 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.002 Å20 Å20 Å2
2---14.889 Å20 Å2
3---7.887 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 291 3643
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005679
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.33661
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5811.5
X-RAY DIFFRACTIONc_mcangle_it2.6172
X-RAY DIFFRACTIONc_scbond_it2.1732
X-RAY DIFFRACTIONc_scangle_it3.0232.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.34

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