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- PDB-1keg: Antibody 64M-2 Fab complexed with dTT(6-4)TT -

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Basic information

Entry
Database: PDB / ID: 1keg
TitleAntibody 64M-2 Fab complexed with dTT(6-4)TT
Components
  • 5'-D(*TP*(64T)P*TP*T)-3'
  • Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain)
  • Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain)
KeywordsIMMUNE SYSTEM/DNA / protein-DNA complex / DNA photoproduct / immunoglobulin / IMMUNE SYSTEM-DNA COMPLEX
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NICKEL (II) ION / DNA
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYokoyama, H. / Mizutani, R. / Satow, Y. / Sato, K. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides.
Authors: Yokoyama, H. / Mizutani, R. / Satow, Y. / Sato, K. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O.
#1: 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.
#2: 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 Ultraviolet-irradiated DNA
Authors: Mori, T. / Nakane, M. / Hattori, T. / Matsunaga, T. / Ihara, M. / Nikaido, O.
History
DepositionNov 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Mar 28, 2012Group: Database references
Revision 1.5Aug 16, 2023Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN There is a C6-C4 bond between 64T residue 2 and T residue 3 of chain A. The 64T linked to ...HETEROGEN There is a C6-C4 bond between 64T residue 2 and T residue 3 of chain A. The 64T linked to T is referred to as DT(6-4)T.
Remark 999SEQUENCE THE NUCLEOTIDE SEQUENCES WHICH ENCODE FOR CHAINS L AND H ARE LISTED IN GB ENTRIES E08525 ...SEQUENCE THE NUCLEOTIDE SEQUENCES WHICH ENCODE FOR CHAINS L AND H ARE LISTED IN GB ENTRIES E08525 (22-330) AND E08524 (7-330) RESPECTIVELY. The residue numbering of chains L and H is non-sequential.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*TP*(64T)P*TP*T)-3'
L: Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain)
H: Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6904
Polymers48,6323
Non-polymers591
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.567, 137.274, 49.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*TP*(64T)P*TP*T)-3'


Mass: 1189.830 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The chain was synthesized by coupling thymidines to both sides of dT(6-4)T which was purified from ultraviolet-radiated dTpT.
#2: Antibody Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain)


Mass: 23762.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: Balb/c
#3: Antibody Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain)


Mass: 23679.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: Balb/c
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, nickel chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2NiCl211
3Tris-HClTris11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→29.6 Å / Num. all: 18057 / Num. obs: 17570 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3 / Num. unique all: 1607 / % possible all: 85.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EHL

1ehl


Resolution: 2.4→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1740 10 %RANDOM
Rwork0.201 ---
all0.207 17221 --
obs0.207 17221 86 %-
Displacement parametersBiso mean: 22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 77 1 70 3456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.44
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.392 62 10.5 %
Rwork0.276 --
obs--29 %

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