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Yorodumi- PDB-1oax: Fv Structure of the IgE SPE-7 in complex with acenaphthenequinone -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oax | ||||||
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Title | Fv Structure of the IgE SPE-7 in complex with acenaphthenequinone | ||||||
Components | (IMMUNOGLOBULIN E) x 2 | ||||||
Keywords | IMMUNE SYSTEM / ANTIBODY-COMPLEX / ANTIBODY / ALLERGY / IGE | ||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / immune response / extracellular space Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | James, L.C. / Roversi, P. / Tawfik, D. | ||||||
Citation | Journal: Science / Year: 2003 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oax.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oax.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 1oax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oax ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oax | HTTPS FTP |
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-Related structure data
Related structure data | 1oaqC 1oarC 1oauC 1oayC 1oazC 1ocwC 1anqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) MUS MUSCULUS (house mouse) / Description: EXPRESSED AS RECOMBINANT FV IN E.COLI / Production host: ESCHERICHIA COLI (E. coli) #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.) MUS MUSCULUS (house mouse) / Description: EXPRESSED AS RECOMBINANT FV IN E.COLI / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01724*PLUS #3: Chemical | #4: 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: 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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: 1.5418 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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