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- PDB-1oax: Fv Structure of the IgE SPE-7 in complex with acenaphthenequinone -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oax | ||||||
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Title | Fv Structure of the IgE SPE-7 in complex with acenaphthenequinone | ||||||
![]() | (IMMUNOGLOBULIN E![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | James, L.C. / Roversi, P. / Tawfik, D. | ||||||
![]() | ![]() Title: Antibody Multispecificity Mediated by Conformational Diversity Authors: James, L.C. / Roversi, P. / Tawfik, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.7 KB | Display | ![]() |
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PDB format | ![]() | 114.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1oaqC ![]() 1oarC ![]() 1oauC ![]() 1oayC ![]() 1oazC ![]() 1ocwC ![]() 1anqS C: citing same article ( 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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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Antibody | ![]() Mass: 13671.359 Da / Num. of mol.: 2 / Fragment: FV REGION, RESIDUES 1-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Antibody | ![]() Mass: 11572.913 Da / Num. of mol.: 4 / Fragment: FV REGION, RESIDUES 1-110 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: 1.5 Å3/Da / Density % sol: 70 % |
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Crystal grow![]() | pH: 5.5 Details: 21% PEG 8K 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.66→39.5 Å / Num. obs: 30262 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rsym value: 0.051 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.67→2.98 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.6 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1ANQ Resolution: 2.67→39.53 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.863 / SU B: 11.63 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY HAS 4 SETS OF 2 CHAINS WHICH ARE RELATED BY NCS. CHAINS I AND K IN THIS ENTRY ARE MOSTLY DISORDERED AND HENCE NO STRUCTURE WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY HAS 4 SETS OF 2 CHAINS WHICH ARE RELATED BY NCS. CHAINS I AND K IN THIS ENTRY ARE MOSTLY DISORDERED AND HENCE NO STRUCTURE WAS CLEARLY DEFINED FOR THESE CHAINS.
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.67→39.53 Å
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Refine LS restraints |
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