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- PDB-6kdi: Antibody 64M-5 Fab including isoAsp in complex with dT(6-4)T -

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Basic information

Entry
Database: PDB / ID: 6kdi
TitleAntibody 64M-5 Fab including isoAsp 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 / isoaspartate
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: 2.7 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: Sci Rep / Year: 2019
Title: Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab.
Authors: Yokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N.
#1: Journal: Acta Crystallogr F Struct Biol Commun / 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.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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

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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)48,4923
Polymers48,4923
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.005, 102.903, 53.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 24097.699 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 / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 15% PEG2000, 0.1 M ammonium sulfate, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 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: 2.7→30 Å / Num. obs: 12638 / % possible obs: 95.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 967 / % possible all: 75

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Processing

Software
NameVersionClassification
CNS1.2refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EHL

1ehl


Resolution: 2.7→27.29 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 57157 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1243 10.3 %RANDOM
Rwork0.21 ---
obs-12045 91 %-
Solvent computationBsol: 32.7839 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 76.4 Å2 / Biso mean: 37.9 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1--10.26 Å20 Å20 Å2
2--4.72 Å20 Å2
3---5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.38 Å
Refinement stepCycle: final / Resolution: 2.7→27.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 37 37 93 3485
Biso mean--35.05 26.47 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.81.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it2.562
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 170 10.7 %
Rwork0.305 1418 -
all-1588 -
obs--74.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3t64b.part64b.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5isoasp.parisoasp.top

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