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- PDB-1i9j: TESTOSTERONE COMPLEX STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD... -

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Basic information

Entry
Database: PDB / ID: 1i9j
TitleTESTOSTERONE COMPLEX STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD TYPE ANTI-TESTOSTERONE FAB FRAGMENT
Components
  • RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT HEAVY CHAIN
  • RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT LIGHT CHAIN
KeywordsIMMUNE SYSTEM / fab fragment / anti-testosterone / recombinant / monoclonal / testosterone
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / metal ion binding
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
TESTOSTERONE / Kappa light chain C_region / Ighg protein / : / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsValjakka, J. / Takkinenz, K. / Teerinen, T. / Soderlund, H. / Rouvinen, J.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structural insights into steroid hormone binding: the crystal structure of a recombinant anti-testosterone Fab fragment in free and testosterone-bound forms.
Authors: Valjakka, J. / Takkinenz, K. / Teerinen, T. / Soderlund, H. / Rouvinen, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: X-ray studies of recombinant anti-testosterone fab fragments: the use of peg 3350 in crystallization
Authors: Valjakka, J. / Hemminki, A. / Teerinen, T. / Takkinen, K. / Rouvinen, J.
History
DepositionMar 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT LIGHT CHAIN
H: RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8553
Polymers47,5662
Non-polymers2881
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-26 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.866, 95.564, 67.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT LIGHT CHAIN


Mass: 24056.625 Da / Num. of mol.: 1
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 RECOMBINANT MONOCLONAL ANTI-TESTOSTERONE FAB FRAGMENT HEAVY CHAIN


Mass: 23509.566 Da / Num. of mol.: 1
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: Q9R1A4, UniProt: Q91Z05*PLUS
#3: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: peg3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlprotein1drop
220 %PEG33501drop
315 %PEG33501drop
40.1 M1dropMgCl2
50.1 MBis-Tris propane1reservoirpH5.6

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: MSC Confocal Blue Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. all: 52788 / Num. obs: 16913 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.299 / % possible all: 95.7
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 52788
Reflection shell
*PLUS
% possible obs: 95.7 % / Mean I/σ(I) obs: 4.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native anti-testosterone fab fragment

Resolution: 2.6→99 Å / σ(F): 1
RfactorNum. reflection
Rfree0.255 1589
Rwork0.188 -
all-15927
obs-14338
Refinement stepCycle: LAST / Resolution: 2.6→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 21 337 3703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_d1.34
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
X-RAY DIFFRACTION5jarkko.paramjarkko.top
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 1 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.34

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