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- PDB-2otu: Crystal structure of Fv polyglutamine complex -

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Basic information

Entry
Database: PDB / ID: 2otu
TitleCrystal structure of Fv polyglutamine complex
Components
  • Fv heavy chain variable domain
  • Fv light chain variable domain
  • peptide antigen
KeywordsIMMUNE SYSTEM / Antibody Fv polyglutamine complex
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLi, P.
CitationJournal: To be Published
Title: Implications of the structure of a poly-Gln/anti-poly-Gln complex for disease progression and therapy
Authors: Li, P.
History
DepositionFeb 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Fv light chain variable domain
B: Fv heavy chain variable domain
C: Fv light chain variable domain
D: Fv heavy chain variable domain
E: Fv light chain variable domain
F: Fv heavy chain variable domain
G: Fv light chain variable domain
H: Fv heavy chain variable domain
P: peptide antigen
Q: peptide antigen
R: peptide antigen
S: peptide antigen


Theoretical massNumber of molelcules
Total (without water)108,59312
Polymers108,59312
Non-polymers00
Water16,718928
1
A: Fv light chain variable domain
B: Fv heavy chain variable domain
P: peptide antigen


Theoretical massNumber of molelcules
Total (without water)27,1483
Polymers27,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fv light chain variable domain
D: Fv heavy chain variable domain
Q: peptide antigen


Theoretical massNumber of molelcules
Total (without water)27,1483
Polymers27,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-12 kcal/mol
Surface area11040 Å2
MethodPISA
3
E: Fv light chain variable domain
F: Fv heavy chain variable domain
R: peptide antigen


Theoretical massNumber of molelcules
Total (without water)27,1483
Polymers27,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Fv light chain variable domain
H: Fv heavy chain variable domain
S: peptide antigen


Theoretical massNumber of molelcules
Total (without water)27,1483
Polymers27,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-13 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.128, 142.681, 75.306
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Fv light chain variable domain


Mass: 12460.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: VL / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody
Fv heavy chain variable domain


Mass: 13330.936 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: VH / Plasmid: pET22b(+) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): BL21 (DE3) / References: UniProt: A2NN81
#3: Protein/peptide
peptide antigen


Mass: 1356.355 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6
Details: 0.1 M sodium citrate, 0.2 M NH4Ac, 27.5% PEG 4000, pH 6.0, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006 / Details: Si(111)
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→41 Å / Num. all: 119617 / Num. obs: 116627 / % possible obs: 97.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.046 / Rsym value: 4.3 / Net I/σ(I): 34.3
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.4 / Num. unique all: 10848 / Rsym value: 25.8 / % possible all: 91.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GSG

2gsg


Resolution: 1.68→41 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 5765 -random
Rwork0.2 ---
all0.2 119819 --
obs0.2 114322 95.4 %-
Refinement stepCycle: LAST / Resolution: 1.68→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7640 0 0 928 8568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.36
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellHighest resolution: 1.68 Å
RfactorNum. reflection
Rfree0.214 5765
Rwork0.2 -
obs-114322

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