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- PDB-1oay: Antibody multispecificity mediated by conformational diversity -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1oay
TitleAntibody multispecificity mediated by conformational diversity
Components(IMMUNOGLOBULIN E) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY-COMPLEX / ANTIBODY / ALLERGY / IGE / CONFORMATIONAL DIVERSITY / MULTISPECIFICITY
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Furazolidone / Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsJames, L.C. / Roversi, P. / Tawfik, D.
CitationJournal: Science / Year: 2003
Title: Antibody Multispecificity Mediated by Conformational Diversity
Authors: James, L.C. / Roversi, P. / Tawfik, D.
History
DepositionJan 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2004Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Oct 30, 2013Group: Source and taxonomy
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: IMMUNOGLOBULIN E
J: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E
M: IMMUNOGLOBULIN E
N: IMMUNOGLOBULIN E
O: IMMUNOGLOBULIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0818
Polymers73,6346
Non-polymers4462
Water5,729318
1
H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4673
Polymers25,2442
Non-polymers2231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
M: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)11,5731
Polymers11,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
J: IMMUNOGLOBULIN E
N: IMMUNOGLOBULIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4673
Polymers25,2442
Non-polymers2231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
O: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)11,5731
Polymers11,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.174, 79.142, 168.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.00184, -1, -0.00212), (-1, -0.00184, 0.00017), (-0.00018, 0.00212, -1)59.2962, 59.1728, 126.7871
2given(-0.00213, -1, -0.00143), (-1, 0.00213, -0.00137), (0.00138, 0.00143, -1)59.3286, 59.1707, 126.8014
3given(0.00207, -1, 0.00197), (-1, -0.00207, -0.00053), (0.00053, -0.00197, -1)58.9614, 59.3651, 126.9268
4given(-0.00841, -0.99992, 0.00917), (-0.99996, 0.00841, -0.0003), (0.00022, -0.00917, -0.99996)58.9366, 58.842, 127.2552

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Components

#1: Antibody IMMUNOGLOBULIN E


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
IMMUNOGLOBULIN E


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 ChemComp-FUR / Furazolidone


Mass: 223.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5N3O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 70 %
Crystal growpH: 7
Details: 0 22% PEG 8K 0.1 M SODIUM CACODYLATE, 0.2M SODIUM ACETATE, PH 5.0
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122 %PEG80001reservoir
20.1 Msodium cacodylate1reservoir
30.2 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2001 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.298→37.268 Å / Num. obs: 47811 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.6
Reflection shellResolution: 2.66→2.81 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.1 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 47809 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.126
Reflection shell
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANQ

1anq


Resolution: 2.66→30 Å / SU B: 5.653 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.206
Details: 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 -5.14 %RANDOM
Rwork0.258 ---
obs0.226 47811 99.4 %-
Displacement parametersBiso mean: 18.638 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.66→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 32 318 5134
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.013
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.248

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