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- PDB-3vw3: Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) ph... -

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Basic information

Entry
Database: PDB / ID: 3vw3
TitleAntibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct
Components
  • (Anti-(6-4) photoproduct antibody 64M-5 Fab ...) x 2
  • DNA (5'-D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3')
KeywordsIMMUNE SYSTEM/DNA / Protein-DNA complex / DNA (6-4) photoproduct / Immunoglobulin / IMMUNE SYSTEM-DNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / COBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYokoyama, H. / Mizutani, R. / Satow, Y.
Citation
Journal: Acta Crystallogr.,Sect.D / 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.
#1: 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.
#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
DepositionJul 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 8, 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9035
Polymers58,7424
Non-polymers1611
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-18 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 68.430, 243.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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DNA chain , 2 types, 2 molecules AB

#3: DNA chain DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3')


Mass: 5638.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA with (6-4) photoproduct
#4: DNA chain DNA (5'-D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3')


Mass: 5396.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA

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Antibody , 2 types, 2 molecules LH

#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 / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#2: Antibody Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)


Mass: 23713.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c

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Non-polymers , 2 types, 145 molecules

#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 3350, 0.1M magnesium acetate, 10mM Cobalt hexamine chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2002 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 20541 / % possible obs: 97.1 % / Redundancy: 10.5 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 60.7
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 16 / % possible all: 97.2

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Processing

Software
NameClassification
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KEG

1keg


Resolution: 2.5→28.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 573129.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1993 9.8 %RANDOM
Rwork0.247 ---
obs0.247 20294 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1259 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 54.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.77 Å20 Å20 Å2
2---7.77 Å20 Å2
3---15.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 732 7 144 4190
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.861.5
X-RAY DIFFRACTIONc_mcangle_it7.012
X-RAY DIFFRACTIONc_scbond_it7.022
X-RAY DIFFRACTIONc_scangle_it9.42.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 322 9.9 %
Rwork0.324 2916 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3t64b.paramt64b.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5nco_xplor_par.txtnco_xplor_top.txt

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