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Yorodumi- PDB-1qd0: CAMELID HEAVY CHAIN VARIABLE DOMAINS PROVIDE EFFICIENT COMBINING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qd0 | ||||||
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Title | CAMELID HEAVY CHAIN VARIABLE DOMAINS PROVIDE EFFICIENT COMBINING SITES TO HAPTENS | ||||||
Components | VHH-R2 ANTI-RR6 ANTIBODY | ||||||
Keywords | IMMUNE SYSTEM / CAMELID VH / IMMUNOGLOBULIN FRAGMENT / AZO-DYE | ||||||
Function / homology | Function and homology information Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Spinelli, S. / Frenken, L.G.J. / Hermans, P. / Verrips, T. / Brown, K. / Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Camelid heavy-chain variable domains provide efficient combining sites to haptens. Authors: Spinelli, S. / Frenken, L.G. / Hermans, P. / Verrips, T. / Brown, K. / Tegoni, M. / Cambillau, C. #1: Journal: Nature / Year: 1993 Title: Naturally Occurring Antibodies Devoid of Light Chains Authors: Hamers-Casterman, C. / Atarhouch, T. / Muyldermans, S. / Robinson, G. / Hamers, C. / Songa, E.B. / Bendahman, N. / Hamers, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qd0.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qd0.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qd0 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qd0 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 13927.599 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN OF A HEAVY CHAIN ANTIBODY / Source method: isolated from a natural source / Source: (natural) Lama glama (llama) / Cell: PERIPHERAL BLOOD LYMPHOCYTE / Tissue: BLOOD / References: GenBank: 4165532, UniProt: A2KD59*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-RR6 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: ammonium sulfate, sodium acetate, glycerol, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 |
Detector | Type: OTHER / Detector: CCD / Date: Apr 29, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 57351 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.25 / % possible all: 62 |
Reflection | *PLUS Num. obs: 8364 / Num. measured all: 57351 |
Reflection shell | *PLUS % possible obs: 62 % |
-Processing
Software |
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Refinement | Resolution: 2.5→12 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→12 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 8157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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