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- PDB-2ok0: Fab ED10-DNA complex -

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Basic information

Entry
Database: PDB / ID: 2ok0
TitleFab ED10-DNA complex
Components
  • 5'-D(*TP*C)-3'
  • Fab ED10 heavy chain
  • Fab ED10 light chain
KeywordsIMMUNE SYSTEM/DNA / immunoglobulin fold / IMMUNE SYSTEM-DNA COMPLEX
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / Mc5 VHCH1 / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsStanfield, R.L. / Sanguineti, S. / Wilson, I.A. / de Prat-Gay, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Specific recognition of a DNA immunogen by its elicited antibody
Authors: Sanguineti, S. / Centeno Crowley, J.M. / Lodeiro Merlo, M.F. / Cerutti, M.L. / Wilson, I.A. / Goldbaum, F.A. / Stanfield, R.L. / de Prat-Gay, G.
History
DepositionJan 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Currently, there is no aminoacid sequence database reference available for the proteins

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*TP*C)-3'
L: Fab ED10 light chain
H: Fab ED10 heavy chain


Theoretical massNumber of molelcules
Total (without water)48,1883
Polymers48,1883
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.711, 63.833, 83.880
Angle α, β, γ (deg.)90.00, 116.26, 90.00
Int Tables number5
Space group name H-MC121
DetailsChains L, H and D (one Fab-DNA complex)

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Components

#1: DNA chain 5'-D(*TP*C)-3'


Mass: 548.417 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Antibody Fab ED10 light chain


Mass: 24148.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS
#3: Antibody Fab ED10 heavy chain


Mass: 23491.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0N7J2*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 6000, 0.05M KCl, 0.01M MgCL2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3MgCL211
4HOH11
5PEG 600012
6KCl12
7MgCL212
8HOH12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.89→40.5 Å / Num. all: 44585 / Num. obs: 44585 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 4.6 / Net I/σ(I): 17.2
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 2106 / Rsym value: 43.3 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→40.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.471 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20358 2235 5 %RANDOM
Rwork0.17687 ---
all0.17825 42211 --
obs0.17825 42211 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.99 Å2
2--0.53 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.89→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 35 0 157 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223479
X-RAY DIFFRACTIONr_bond_other_d0.0030.022306
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9644750
X-RAY DIFFRACTIONr_angle_other_deg0.9263.0035646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16624.403134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4041511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
X-RAY DIFFRACTIONr_nbd_refined0.1980.2669
X-RAY DIFFRACTIONr_nbd_other0.220.22596
X-RAY DIFFRACTIONr_nbtor_refined0.2050.21846
X-RAY DIFFRACTIONr_nbtor_other0.1030.22213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.27
X-RAY DIFFRACTIONr_mcbond_it1.2461.52498
X-RAY DIFFRACTIONr_mcbond_other0.2641.5872
X-RAY DIFFRACTIONr_mcangle_it1.64323533
X-RAY DIFFRACTIONr_scbond_it2.78431524
X-RAY DIFFRACTIONr_scangle_it3.8764.51217
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 157 -
Rwork0.307 2943 -
obs-2943 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.87691.49180.25911.9664-0.05142.2703-0.03230.22380.1083-0.1149-0.0242-0.1811-0.07880.12010.0565-0.17330.0395-0.022-0.23960.0149-0.154466.71568.305733.6833
23.0979-1.9861.39145.2264-2.21434.52680.09850.0715-0.17310.00530.04550.08720.18140.2635-0.144-0.23270.01050.0224-0.1854-0.0093-0.186496.239957.979250.2595
34.0306-0.4442.02692.218-1.07523.56430.0075-0.2945-0.13930.16410.01350.05240.178-0.1307-0.021-0.19010.0046-0.0047-0.235-0.0193-0.169157.093359.965751.2041
46.19431.7268-2.89133.4555-1.43418.08520.1373-0.34360.0575-0.0347-0.0087-0.3607-0.52590.5552-0.1286-0.1259-0.01220.0311-0.16-0.0077-0.193892.396166.26863.0264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LB1 - 1121 - 117
2X-RAY DIFFRACTION2LB113 - 214118 - 219
3X-RAY DIFFRACTION3HC1 - 1161 - 119
4X-RAY DIFFRACTION3DA1 - 21 - 2
5X-RAY DIFFRACTION4HC117 - 228120 - 216

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