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- PDB-1ehl: 64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T -

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Basic information

Entry
Database: PDB / ID: 1ehl
Title64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T
Components
  • 5'-(D(5HT)P*(6-4)T)-3'
  • ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (HEAVY CHAIN)
  • ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / PROTEIN-DNA COMPLEX / DNA PHOTOPRODUCT
Function / homology
Function and homology information


immunoglobulin receptor binding / B cell differentiation / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / Immunoglobulin kappa constant / Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsYokoyama, H. / Mizutani, R. / Satow, Y. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation.
Authors: Yokoyama, H. / Mizutani, R. / Satow, Y. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O.
#1: Journal: Photochem.Photobiol. / Year: 1991
Title: Simultaneous Establishment of Monoclonal Antibodies Specific for Either Cyclobutane Pyrimidine Dimer or (6-4)photoproduct from the Same Mouse Immunized with Ultraviolet-Irradiated DNA
Authors: Mori, T. / Nakane, M. / Hattori, T. / Matsunaga, T. / Ihara, M. / Nikaido, O.
#2: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1998
Title: Antibodies Specific for (6-4) DNA Photoproducts: Cloning, Antibody Modeling and Construction of a Single-Chain Fv Derivative
Authors: Morioka, H. / Miura, H. / Kobayashi, H. / Koizumi, T. / Fujii, K. / Asano, K. / Matsunaga, T. / Nikaido, O. / Stewart, J.D. / Ohtsuka, E.
History
DepositionFeb 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-(D(5HT)P*(6-4)T)-3'
L: ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (LIGHT CHAIN)
H: ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,9153
Polymers47,9153
Non-polymers00
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.500, 48.062, 77.939
Angle α, β, γ (deg.)90.00, 104.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain 5'-(D(5HT)P*(6-4)T)-3'


Mass: 501.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Purified from ultraviolet-radiated dTpT
#2: Antibody ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (LIGHT CHAIN)


Mass: 23891.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: UniProt: P01837*PLUS
#3: Antibody ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (HEAVY CHAIN)


Mass: 23522.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: UniProt: P01863*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, nickel chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Temperature: 20 ℃ / PH range low: 8.4 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.2 mM64M-2 Fab1drop
20.25 mMdT(6-4)T1drop
314-18 %(w/v)PEG80001reservoir
40.1 MHEPES-Na1reservoiror Tris-HCl, pH7.5-8.4
510 mM1reservoirNiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 26, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→28.7 Å / Num. all: 77929 / Num. obs: 18790 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.221 / Num. unique all: 1571 / % possible all: 79.1
Reflection
*PLUS
Num. measured all: 77929
Reflection shell
*PLUS
% possible obs: 79.1 % / Num. unique obs: 1571 / Num. measured obs: 4271 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementResolution: 2.4→10 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1824 -RANDOM
Rwork0.192 ---
all0.199 18504 --
obs0.199 18484 91.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 37 0 360 3715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.871
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / σ(F): 1 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rfactor Rfree: 0.359 / Rfactor obs: 0.296

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