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- PDB-6kdh: Antibody 64M-5 Fab including isoAsp in ligand-free form -

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Basic information

Entry
Database: PDB / ID: 6kdh
TitleAntibody 64M-5 Fab including isoAsp in ligand-free form
Components
  • Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)
  • Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)
KeywordsIMMUNE SYSTEM / DNA (6-4) PHOTOPRODUCT / IMMUNOGLOBULIN / FAB / isoaspartate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.47 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)


Theoretical massNumber of molelcules
Total (without water)47,9262
Polymers47,9262
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-26 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.789, 150.485, 65.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11H-392-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 8% PEG3350, 8% isopropanol, 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: Apr 4, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.47→30 Å / Num. obs: 17039 / % possible obs: 92.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.8
Reflection shellResolution: 2.47→2.55 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1271 / % possible all: 73.4

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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: 2.47→29.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 229792 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1668 9.8 %RANDOM
Rwork0.194 ---
obs-17025 92.6 %-
Solvent computationBsol: 31.6527 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 91.57 Å2 / Biso mean: 33.4 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0 Å20 Å2
2--2.95 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: final / Resolution: 2.47→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 0 241 3586
Biso mean---35.1 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_mcangle_it3.092
X-RAY DIFFRACTIONc_scbond_it2.992
X-RAY DIFFRACTIONc_scangle_it4.152.5
LS refinement shellResolution: 2.47→2.62 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 190 7.7 %
Rwork0.273 2275 -
all-2465 -
obs--81.9 %
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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