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- PDB-6idg: antibody 64M-5 Fab in complex with dT(6-4)T -

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Basic information

Entry
Database: PDB / ID: 6idg
Titleantibody 64M-5 Fab in complex with dT(6-4)T
Components
  • Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)
  • Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)
  • DNA (5'-D(*(64T)P*(5PY))-3')
KeywordsIMMUNE SYSTEM / DNA (6-4) PHOTOPRODUCT / IMMUNOGLOBULIN / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DNA
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K07316 Japan
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms.
Authors: Yokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab
Authors: Yokoyama, H. / Mizutani, R. / Satow, Y.
#2: 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.
History
DepositionSep 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,3883
Polymers48,3883
Non-polymers00
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.620, 100.865, 51.666
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: Antibody Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)


Mass: 23993.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma / Strain: BALB/c
#2: Antibody Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)


Mass: 23828.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma / Strain: BALB/c
#3: DNA chain DNA (5'-D(*(64T)P*(5PY))-3')


Mass: 565.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG2000, 0.5 M lithium sulfate, 0.1 M sodium citrate (pH 3.5)

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 22, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 27037 / % possible obs: 88.2 % / Redundancy: 11.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 31.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 2018 / % possible all: 66.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EHL

1ehl


Resolution: 2→28.18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 72552.57 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2596 9.9 %RANDOM
Rwork0.192 ---
obs0.192 26313 86 %-
Solvent computationBsol: 56.1635 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1--6.52 Å20 Å20 Å2
2---7.29 Å20 Å2
3---13.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: 1 / Resolution: 2→28.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 37 0 383 3780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 332 9.9 %
Rwork0.233 3007 -
obs--66.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3~/64m5ds18/cns/toppar/t64b.par~/64m5ds18/cns/toppar/t64b.top
X-RAY DIFFRACTION4CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top

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