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- PDB-1oaq: Free conformation Ab1 of the IgE SPE-7 -

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Basic information

Entry
Database: PDB / ID: 1oaq
TitleFree conformation Ab1 of the IgE SPE-7
Components
  • HEAVY CHAIN
  • LIGHT CHAIN
KeywordsIMMUNE SYSTEM / 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
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: 1.5 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 1.1Oct 30, 2013Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / 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
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 / _pdbx_entry_details.has_protein_modification
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

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Assembly

Deposited unit
H: HEAVY CHAIN
L: LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)26,1292
Polymers26,1292
Non-polymers00
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-14 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.541, 70.743, 82.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody HEAVY CHAIN


Mass: 13616.237 Da / Num. of mol.: 1 / Fragment: FV, RESIDUES 1-121
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 LIGHT CHAIN


Mass: 12512.920 Da / Num. of mol.: 1 / Fragment: FV, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01724*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNEW SEQUENCE

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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: 5
Details: 1.2M NA CITRATE 0.2M NA CACODYLATE PH5, 0.2M LITHIUM, pH 5.00
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1 M / Common name: sodium citrate / Details: pH6.2

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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, 2000 / 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: 1.5→33.3 Å / Num. obs: 34286 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.6 / % possible all: 91.7
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 34284 / % possible obs: 92.8 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.0431
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 92.8 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 1.2

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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: 1.5→33.33 Å / SU B: 1.136 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.18167 1734 5.1 %RANDOM
Rwork0.15965 ---
obs0.15965 32550 97.2 %-
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: 1.5→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 0 275 2037
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.005
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.175 / Rfactor Rwork: 0.155

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