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Yorodumi- PDB-1sjx: Three-Dimensional Structure of a Llama VHH Domain OE7 binding the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sjx | ||||||
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Title | Three-Dimensional Structure of a Llama VHH Domain OE7 binding the cell wall protein Malf1 | ||||||
Components | immunoglobulin VH domain | ||||||
Keywords | IMMUNE SYSTEM / Camelids antibody / heavy chain / dandruff / phage display | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dolk, E. / van der Vaart, M. / Hulsik, D.L. / Vriend, G. / de Haard, H. / Spinelli, S. / Cambillau, C. / Frenken, L. / Verrips, T. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2005 Title: Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo. Authors: Dolk, E. / van der Vaart, M. / Hulsik, D.L. / Vriend, G. / de Haard, H. / Spinelli, S. / Cambillau, C. / Frenken, L. / Verrips, T. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the protein was not deposited into any sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sjx.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sjx.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 1sjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sjx_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 1sjx_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 1sjx_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1sjx_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/1sjx ftp://data.pdbj.org/pub/pdb/validation_reports/sj/1sjx | HTTPS FTP |
-Related structure data
Related structure data | 1hcvS S: Starting model for refinement |
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Similar 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: 13214.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Description: Protein selected by phage display / Cell: lymphocytes / Production host: Saccharomyces cerevisiae (brewer's yeast) | ||
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#2: Chemical | #3: 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: 4.17 Å3/Da / Density % sol: 70.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 10% PEG 6K, 100mM Hepes, 5% MPD, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24 Å / Num. obs: 11594 / % possible obs: 99.8 % / Observed criterion σ(F): 3.5 / Observed criterion σ(I): 3.5 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1637 / Rsym value: 0.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HCV Resolution: 2.2→24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.613 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.165 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.713 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.199→2.256 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: -2.283 Å / Origin y: 49.94 Å / Origin z: 5.464 Å
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