+Open data
-Basic information
Entry | Database: PDB / ID: 1x9q | ||||||
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Title | 4m5.3 anti-fluorescein single chain antibody fragment (scFv) | ||||||
Components | 4m5.3 anti-fluorescein single chain antibody fragment | ||||||
Keywords | IMMUNE SYSTEM / very high affinity / antibody binding / electrostatics / directed evolution / single chain antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Midelfort, K.S. / Hernandez, H.H. / Lippow, S.M. / Tidor, B. / Drennan, C.L. / Wittrup, K.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody Authors: Midelfort, K.S. / Hernandez, H.H. / Lippow, S.M. / Tidor, B. / Drennan, C.L. / Wittrup, K.D. | ||||||
History |
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Remark 999 | SEQUENCE The flag tag has 14 residues (1-14). Residues 15-126 correspond to VL. There is a 25- ...SEQUENCE The flag tag has 14 residues (1-14). Residues 15-126 correspond to VL. There is a 25-residue linker (residues 127-151). Residues 152-268 correspond to VH. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x9q.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x9q.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 1x9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/1x9q ftp://data.pdbj.org/pub/pdb/validation_reports/x9/1x9q | HTTPS FTP |
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-Related structure data
Related structure data | 1flrS 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: 29482.742 Da / Num. of mol.: 1 / Fragment: antibody binding fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: GAL1-10 promoter / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YVH10 | ||||
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#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-FLU / | #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: 2.15 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.15 M Sodium Acetate, 0.1 M Ammonium Acetate, 20% PEG 4000, 10% Glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.984 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 40648 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rsym value: 0.03 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1FLR Resolution: 1.5→28.75 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: Of 268 residues, residues 14-268 were observed in electron density maps, with one chain break from residues 125-148.
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Refinement step | Cycle: LAST / Resolution: 1.5→28.75 Å
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