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Open data
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Basic information
Entry | Database: PDB / ID: 1kfa | ||||||
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Title | Crystal structure of Fab fragment complexed with gibberellin A4 | ||||||
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![]() | IMMUNE SYSTEM / Immunoglobuiln fold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / GIBBERELLIN A4![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murata, T. / Fushinobu, S. / Nakajima, M. / Asami, O. / Sassa, T. / Wakagi, T. / Yamaguchi, I. | ||||||
![]() | ![]() Title: Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment. Authors: Murata, T. / Fushinobu, S. / Nakajima, M. / Asami, O. / Sassa, T. / Wakagi, T. / Yamaguchi, I. #1: ![]() Title: Monoclonal antibodies specific for non-derivatized gibberellins I Authors: Nakajima, M. / Yamaguchi, I. / Nagatani, A. / Kizawa, S. / Murofushi, N. / Furuya, N. / Takahashi, N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.6 KB | Display | ![]() |
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PDB format | ![]() | 131.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 595.7 KB | Display | ![]() |
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Full document | ![]() | 630.2 KB | Display | |
Data in XML | ![]() | 36.8 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ikfS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23754.285 Da / Num. of mol.: 2 / Fragment: residues 1-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 23760.887 Da / Num. of mol.: 2 / Fragment: Variable domain, constant domain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.62 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→39.62 Å / Num. all: 402565 / Num. obs: 402565 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3799 / Rsym value: 0.321 / % possible all: 99.7 |
Reflection | *PLUS Num. obs: 26460 / % possible obs: 100 % / Num. measured all: 402565 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ikf Resolution: 2.8→39.62 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1685086.35 / Data cutoff low absF: 0 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.0048 Å2 / ksol: 0.373888 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→39.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Num. reflection obs: 22549 / % reflection Rfree: 5 % / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.234 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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