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Yorodumi- PDB-1shm: Convergent solutions to VHH domain stabilization from natural and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1shm | ||||||
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Title | Convergent solutions to VHH domain stabilization from natural and in vitro evolution | ||||||
Components | ANTIBODY RIG | ||||||
Keywords | IMMUNE SYSTEM / Heavy Chain Variable Domain / VHH Domain / Immunoglobulin | ||||||
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: 1.9 Å | ||||||
Authors | Bond, C.J. / Wiesmann, C. / Marsters, J.C. / Sidhu, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: A structure-based database of antibody variable domain diversity. Authors: Bond, C.J. / Wiesmann, C. / Marsters, J.C. / Sidhu, S.S. | ||||||
History |
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Remark 999 | SEQUENCE The original gene for the protein was cloned from llama (GB 4165492). One loop (residues ...SEQUENCE The original gene for the protein was cloned from llama (GB 4165492). One loop (residues 96-101, sequence: RIGRSVFNLRRESWVTW) replaces the natural sequence with an engineered sequence. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1shm.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1shm.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 1shm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1shm_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 1shm_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 1shm_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1shm_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/1shm ftp://data.pdbj.org/pub/pdb/validation_reports/sh/1shm | 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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Unit cell |
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Details | The relevant biological assembly is one VH domain. The asymmetric unit is composed of 4 independent VH domains. |
-Components
#1: Antibody | Mass: 13680.156 Da / Num. of mol.: 4 / Fragment: RIG VHH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #2: 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: 2.09 Å3/Da / Density % sol: 40.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 4K, 0.3M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Aug 15, 2003 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 32402 / Num. obs: 32305 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HCV Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.468 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.161 / 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: 17.292 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.939 Å / Total num. of bins used: 25 /
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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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