+Open data
-Basic information
Entry | Database: PDB / ID: 3lrg | ||||||
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Title | Structure of anti-huntingtin VL domain | ||||||
Components | anti-huntingtin VL domain | ||||||
Keywords | IMMUNE SYSTEM / Huntington's disease / Huntingtin / Variable light chain domain / Intrabody / Immunoglobulin | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Schiefner, A. / Chatwell, L. / Skerra, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: A Disulfide-Free Single-Domain V(L) Intrabody with Blocking Activity towards Huntingtin Reveals a Novel Mode of Epitope Recognition. Authors: Schiefner, A. / Chatwell, L. / Korner, J. / Neumaier, I. / Colby, D.W. / Volkmer, R. / Wittrup, K.D. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lrg.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lrg.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lrg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/3lrg ftp://data.pdbj.org/pub/pdb/validation_reports/lr/3lrg | HTTPS FTP |
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-Related structure data
Related structure data | 3lrhC 1mfaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 12860.970 Da / Num. of mol.: 2 / Fragment: anti-huntingtin VL domain / Mutation: G112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: Phage display library / synthetic / Gene: VL12.3 / Plasmid: pASK75(T7RBS)his / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 #2: Chemical | ChemComp-TRS / | #3: Chemical | ChemComp-IMD / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.8 Details: 1.2 M Ammonium sulfate, 0.2 M Sodium chloride, 0.1 M CHES-NAOH, pH 9.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 13, 2006 |
Radiation | Monochromator: Osmic confocal Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 19201 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 11.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MFA Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.062 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.101 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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