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- PDB-1i8m: CRYSTAL STRUCTURE OF A RECOMBINANT ANTI-SINGLE-STRANDED DNA ANTIB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i8m | ||||||
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Title | CRYSTAL STRUCTURE OF A RECOMBINANT ANTI-SINGLE-STRANDED DNA ANTIBODY FRAGMENT COMPLEXED WITH DT5 | ||||||
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![]() | IMMUNE SYSTEM/DNA / fab / antibody / anti-DNA antibody / autoantibody / lupus / IMMUNE SYSTEM-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanner, J.J. / Komissarov, A.A. / Deutscher, S.L. | ||||||
![]() | ![]() Title: Crystal Structure of an Antigen-Binding Fragment Bound to Single-Stranded DNA Authors: Tanner, J.J. / Komissarov, A.A. / Deutscher, S.L. #1: ![]() Title: Crystallization and Molecular Replacement Studies of a Recombinant Antigen-Binding Fragment Complexed with Single-stranded DNA. Authors: Prewitt, S.P. / Komissarov, A.A. / Deutscher, S.L. / Tanner, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184 KB | Display | ![]() |
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PDB format | ![]() | 143.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.4 KB | Display | ![]() |
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Full document | ![]() | 485.4 KB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mlcS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is an antigen binding fragment, Fab. There are two Fabs in the asymmetric unit. |
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Components
-DNA chain , 2 types, 2 molecules TD
#1: DNA chain | Mass: 1476.007 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 563.428 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Antibody , 2 types, 4 molecules LAHB
#3: Antibody | Mass: 23616.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Antibody | Mass: 24153.158 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 2 types, 340 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 2 M ammonium sulfate, 0.1 M sodium acetate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / PH range low: 5.2 / PH range high: 4.8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.1→28 Å / Num. all: 72520 / Num. obs: 72520 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.3 | ||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3.6 / % possible all: 96 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 28 Å / % possible obs: 98.8 % / Num. measured all: 489562 | ||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 95.9 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1mlc Resolution: 2.1→27.66 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3972329.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.21 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→27.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.219 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.5 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.304 / % reflection Rfree: 9.3 % / Rfactor obs: 0.274 |