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- PDB-1xf2: Structure of Fab DNA-1 complexed with dT3 -

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Basic information

Entry
Database: PDB / ID: 1xf2
TitleStructure of Fab DNA-1 complexed with dT3
Components
  • 5'-D(*TP*TP*T)-3'
  • antibody heavy chain Fab
  • antibody light chain Fab
KeywordsIMMUNE SYSTEM/DNA / antibody / Fab / immunoglobulin / anti-DNA / anti-ssDNA / autoantibody / IMMUNE SYSTEM-DNA COMPLEX
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : / DNA
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchuermann, J.P. / Prewitt, S.P. / Deutscher, S.L. / Tanner, J.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Evidence for Structural Plasticity of Heavy Chain Complementarity-determining Region 3 in Antibody-ssDNA Recognition
Authors: Schuermann, J.P. / Prewitt, S.P. / Davies, C. / Deutscher, S.L. / Tanner, J.J.
History
DepositionSep 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
T: 5'-D(*TP*TP*T)-3'
L: antibody light chain Fab
H: antibody heavy chain Fab
A: antibody light chain Fab
B: antibody heavy chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2567
Polymers98,0645
Non-polymers1922
Water3,963220
1
T: 5'-D(*TP*TP*T)-3'
L: antibody light chain Fab
H: antibody heavy chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5624
Polymers49,4663
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: antibody light chain Fab
B: antibody heavy chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6943
Polymers48,5982
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.678, 170.678, 144.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is Fab, which has one light chain and one heavy chain

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Components

#1: DNA chain 5'-D(*TP*TP*T)-3'


Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Antibody antibody light chain Fab / anti-single-stranded dna antigen-binding fab


Mass: 23616.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 498315
#3: Antibody antibody heavy chain Fab / anti-single-stranded dna antigen-binding fab


Mass: 24982.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 3399661
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.2 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ammonium sulfate, sodium phosphate, sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2sodium phosphate11
3sodium citrate11
4H2O11
5ammonium sulfate12
6sodium phosphate12
7sodium citrate12

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 1, 2002
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→29.5 Å / Num. all: 55433 / Num. obs: 55433 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 31
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.446 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I8M

1i8m


Resolution: 2.3→29.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.09 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24194 2752 5 %RANDOM
Rwork0.20157 ---
all0.20354 55433 --
obs0.20354 55433 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.429 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å20 Å2
2--0.84 Å20 Å2
3----1.26 Å2
Refine analyzeLuzzati sigma a free: 0.13 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6449 41 10 220 6720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216675
X-RAY DIFFRACTIONr_bond_other_d0.0020.025718
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9589111
X-RAY DIFFRACTIONr_angle_other_deg0.829313410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027362
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021288
X-RAY DIFFRACTIONr_nbd_refined0.180.21405
X-RAY DIFFRACTIONr_nbd_other0.2480.26535
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1280.24901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6021.54244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17526874
X-RAY DIFFRACTIONr_scbond_it1.79732431
X-RAY DIFFRACTIONr_scangle_it2.8464.52237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 182
Rwork0.216 3791
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.07591.02960.97640.99460.50620.79110.03890.06310.2467-0.02280.02060.1138-0.1261-0.2505-0.05950.22020.05010.05820.35620.05470.337486.21895.889-14.893
22.8009-1.1961-0.24512.8938-0.39920.9064-0.0802-0.26360.24450.00920.0683-0.4481-0.11950.36950.01190.1786-0.04850.00310.4603-0.13110.328274.56498.71220.23
31.6304-0.956-1.43071.22231.29043.49810.06980.07530.1366-0.0950.02620.0307-0.15660.061-0.0960.3269-0.0250.0160.27840.02490.2849118.56595.331-33.717
44.65552.7997-2.29612.8292-2.21672.71880.1603-0.53350.35090.3787-0.04880.1395-0.21730.0951-0.11150.36520.03070.05280.3385-0.11050.238140.4798.66637.251
52.1951-0.2688-0.54891.87980.6624.14970.0938-0.131-0.07670.16870.06250.0509-0.0356-0.1003-0.15640.2020.0072-0.04710.34960.04490.299586.56873.576-19.785
63.505-0.3563-0.93172.9407-0.18262.82520.0342-0.1596-0.1153-0.01970.0512-0.36110.25170.3581-0.08540.19190.1369-0.06290.4169-0.03610.255672.52876.64922.309
72.65190.59530.40122.43170.71021.01890.0147-0.0016-0.0134-0.069-0.00910.1096-0.2057-0.0575-0.00570.2869-0.0166-0.01850.28150.00960.2525119.12882.209-23.781
83.7415-0.9729-0.0922.50020.07641.1656-0.1047-0.1364-0.02570.16710.10730.0399-0.16640.04-0.00260.29290.03110.00950.27240.01080.22840.34586.95225.76
924.03872.589-7.77856.4901-2.16543.2113-0.8193-0.7797-0.4970.0043-0.21670.0910.0858-0.03091.0360.05520.05320.08320.18220.0410.175872.25586.181-7.425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LB1 - 1081 - 108
2X-RAY DIFFRACTION2AD1 - 1081 - 108
3X-RAY DIFFRACTION3LB109 - 213109 - 213
4X-RAY DIFFRACTION4AD109 - 213109 - 213
5X-RAY DIFFRACTION5HC1 - 1131 - 120
6X-RAY DIFFRACTION6BE1 - 1131 - 120
7X-RAY DIFFRACTION7HC114 - 213121 - 220
8X-RAY DIFFRACTION8BE114 - 213121 - 220
9X-RAY DIFFRACTION9TA1 - 31 - 3

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