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- PDB-1i9i: NATIVE CRYSTAL STRUCTURE OF THE RECOMBINANT MONOCLONAL WILD TYPE ... -

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Basic information

Entry
Database: PDB / ID: 1i9i
TitleNATIVE CRYSTAL 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
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Kappa light chain C_region / Ighg protein / : / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.72 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)47,5662
Polymers47,5662
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-25 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.461, 90.850, 137.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: peg3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
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 RU200HB / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: MSC Confocal Blue Optics
RadiationMonochromator: MSC Confocal Blue Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.72→99 Å / Num. all: 103739 / Num. obs: 15557 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.72→2.82 Å / Rmerge(I) obs: 0.304 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 103739
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 4.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab fragment 4-4-20

Resolution: 2.72→99 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.252 1428 -
Rwork0.195 --
all-15566 -
obs-14496 93.1 %
Refinement stepCycle: LAST / Resolution: 2.72→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 0 88 3433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_d1.4
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
Lowest resolution: 500 Å / σ(F): 1 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4

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