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- PDB-2fr4: Structure of Fab DNA-1 complexed with a stem-loop DNA ligand -

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Basic information

Entry
Database: PDB / ID: 2fr4
TitleStructure of Fab DNA-1 complexed with a stem-loop DNA ligand
Components
  • 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-3'
  • antibody heavy chain FAB
  • antibody light chain FAB
KeywordsIMMUNE SYSTEM/DNA / ANTIBODY / FAB / IMMUNOGLOBULIN / ANTI-DNA / ANTI-SSDNA / AUTOANTIBODY / stem-loop DNA / 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: 1.95 Å
AuthorsTanner, J.J. / Ou, Z.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Impact of DNA hairpin folding energetics on antibody-ssDNA association.
Authors: Ou, Z. / Bottoms, C.A. / Henzl, M.T. / Tanner, J.J.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN PEG, DI(HYDROXYETHYL)ETHER WAS USED FOR CRYSTALLIZATION. ONLY THE FRAGMENT, PG4 WAS OBSERVED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-3'
N: 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-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)103,3827
Polymers103,1886
Non-polymers1941
Water7,206400
1
M: 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-3'
A: antibody light chain FAB
B: antibody heavy chain FAB


Theoretical massNumber of molelcules
Total (without water)51,5943
Polymers51,5943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-3'
L: antibody light chain FAB
H: antibody heavy chain FAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7884
Polymers51,5943
Non-polymers1941
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.757, 90.450, 128.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is an antigen-binding fragment, which consists of one light chain and one heavy chain. There are two biological assemblies in the asymmetric unit: LH and AB.

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Components

#1: DNA chain 5'-D(*CP*TP*GP*CP*CP*TP*TP*CP*AP*G)-3'


Mass: 2995.967 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: single-stranded DNA oligonucleotide synthesized by IDT
#2: Antibody antibody light chain FAB


Mass: 23616.057 Da / Num. of mol.: 2 / Fragment: antigen-binding fragment
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


Mass: 24982.039 Da / Num. of mol.: 2 / Fragment: antigen-binding fragment
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris-HCL, 12-26% (w/v) PEGMME 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCL11
2PEGMME 200011
3H2O11
4PEGMME 200012
5H2O12

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorDetector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 70761 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.052 / Χ2: 0.976 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
1.95-2.0297.13.70.4269750.9451
2.02-2.199.640.3271460.9761
2.1-2.299.74.10.22671590.9391
2.2-2.3199.84.10.17871710.9691
2.31-2.4699.44.10.13671580.9771
2.46-2.6599.24.10.09271660.991
2.65-2.9198.64.10.06271530.991
2.91-3.3397.74.10.04471060.981
3.33-4.295.840.03670300.9911
4.2-5087.74.10.03266970.9971

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1I8M

1i8m


Resolution: 1.95→22.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.819 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3596 5.1 %RANDOM
Rwork0.207 ---
all0.21 ---
obs0.21 70706 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.402 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.95→22.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 396 8 400 7283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227106
X-RAY DIFFRACTIONr_bond_other_d0.0010.025924
X-RAY DIFFRACTIONr_angle_refined_deg1.5412.0279768
X-RAY DIFFRACTIONr_angle_other_deg0.828313913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9625847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89824.435248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.046151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5411516
X-RAY DIFFRACTIONr_chiral_restr0.0870.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021295
X-RAY DIFFRACTIONr_nbd_refined0.1810.21120
X-RAY DIFFRACTIONr_nbd_other0.1810.25793
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23311
X-RAY DIFFRACTIONr_nbtor_other0.0860.24143
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2415
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.29
X-RAY DIFFRACTIONr_mcbond_it0.7641.54512
X-RAY DIFFRACTIONr_mcbond_other0.1771.51723
X-RAY DIFFRACTIONr_mcangle_it1.15526891
X-RAY DIFFRACTIONr_scbond_it1.66733346
X-RAY DIFFRACTIONr_scangle_it2.2994.52877
LS refinement shellResolution: 1.948→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 265 -
Rwork0.267 4791 -
obs-5056 100 %
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)
15.39793.599-0.78995.20462.33636.12780.9941-1.02940.33721.0833-0.4304-0.1469-0.53570.8013-0.56370.2187-0.37970.05480.1336-0.1253-0.091498.735529.030729.4166
24.98843.7132-1.51775.1486-0.5194.01720.2085-0.9954-0.25730.269-0.2136-0.2748-0.17891.03360.0051-0.0215-0.0068-0.01650.15730.0108-0.173674.12413.766751.4058
31.98110.9941-0.02893.15173.25210.9965-0.1740.2662-0.2944-0.38910.0369-0.2775-0.00521.26720.1371-0.23190.0370.08630.1002-0.0173-0.0194111.04845.3807-25.8221
46.73930.67281.12741.50660.5533.1435-0.44770.64730.3244-0.54720.5661-0.0055-0.97640.1463-0.11840.2764-0.19590.16720.0063-0.0735-0.027884.59063.2546-50.5858
52.962.0279-0.80094.54190.48133.72030.0568-0.06440.18150.11430.01390.2769-0.26740.1247-0.0707-0.2652-0.0195-0.0119-0.24170.0143-0.204888.433416.909913.6784
63.01420.4741-0.07272.69780.69756.00250.0061-0.29110.24980.22490.05880.1065-0.47930.0954-0.0649-0.05850.00950.0273-0.20310.0066-0.165463.342718.843440.3296
75.03740.39960.92221.9730.58324.02870.0219-0.0249-0.45130.013-0.19560.00880.26020.05850.1737-0.22170.01860.0471-0.1965-0.0512-0.119294.53364.8975-11.0992
81.4994-0.6617-2.15932.93723.88318.02070.06110.00640.1077-0.41110.2058-0.2271-0.22590.192-0.2669-0.1553-0.04430.0274-0.1406-0.0851-0.13380.5946-9.7663-41.684
93.8436-1.7716-1.58498.50588.05979.99370.2879-1.00570.25890.110.2562-0.7232-0.26581.2911-0.54410.139-0.30850.10180.3544-0.06620.0365108.48622.0767.4165
1014.58731.7201-7.37051.15621.657310.41910.9701-0.9420.67321.1308-0.6809-1.16690.07621.681-0.28920.0611-0.143-0.05630.36980.0387-0.0409112.204514.3478-3.0415
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AE1 - 1081 - 108
22AE109 - 213109 - 213
33LC2 - 1082 - 108
44LC109 - 213109 - 213
55BF1 - 1131 - 120
66BF114 - 213121 - 220
77HD1 - 1131 - 120
88HD114 - 213121 - 220
99MA5 - 141 - 10
1010NB5 - 141 - 10

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