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Yorodumi- PDB-1i3u: THREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i3u | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF A LLAMA VHH DOMAIN COMPLEXED WITH THE DYE RR1 | ||||||
Components | ANTIBODY VHH LAMA DOMAIN | ||||||
Keywords | IMMUNE SYSTEM / antibody / VHH fragment / Lama glama | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-RR1 Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Spinelli, S. / Tegoni, M. / Frenken, L. / van Vliet, C. / Cambillau, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Lateral recognition of a dye hapten by a llama VHH domain. Authors: Spinelli, S. / Tegoni, M. / Frenken, L. / van Vliet, C. / Cambillau, C. | ||||||
History |
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Remark 999 | SEQUENCE AN APPROPRIATE SEQUENCE DATABASE MATCH WAS NOT AVAILABLE AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i3u.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i3u.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 1i3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i3u_validation.pdf.gz | 894.3 KB | Display | wwPDB validaton report |
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Full document | 1i3u_full_validation.pdf.gz | 899.9 KB | Display | |
Data in XML | 1i3u_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1i3u_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/1i3u ftp://data.pdbj.org/pub/pdb/validation_reports/i3/1i3u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 13842.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-RR1 / |
#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: 3.65 Å3/Da / Density % sol: 66.27 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: MME 5000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: ID2 / Wavelength: 0.988 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 189080 / Num. obs: 15022 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 1088 / Rsym value: 0.144 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 189080 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.144 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: VHH52 anti-R1 unliganded Resolution: 1.95→18.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2310814.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.87 Å2 / ksol: 0.364 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→18.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / 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 / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.305 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.29 |