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- PDB-1ocw: Free conformation Ab2 of the IgE SPE-7 -

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Basic information

Entry
Database: PDB / ID: 1ocw
TitleFree conformation Ab2 of the IgE SPE-7
Components(IMMUNOGLOBULIN E) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY / ALLERGY / 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: 2 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
DepositionFeb 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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
L: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)26,2012
Polymers26,2012
Non-polymers00
Water1,22568
1
H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E

H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E

H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E

H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)104,8058
Polymers104,8058
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area18290 Å2
ΔGint-105.4 kcal/mol
Surface area41940 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.545, 79.545, 67.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Antibody IMMUNOGLOBULIN E


Mass: 13616.237 Da / Num. of mol.: 1 / Fragment: FV REGION, 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 IMMUNOGLOBULIN E


Mass: 12584.981 Da / Num. of mol.: 1 / Fragment: FV REGION, RESIDUES 1-120
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 40 %
Crystal growpH: 5 / Details: 0.1M HEPES, PH7.5, 70% MPD, pH 5.00

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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: Aug 15, 2002 / 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: 2.01→28.17 Å / Num. obs: 13952 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAQ

1oaq


Resolution: 2→28.17 Å
Details: REFINEMENT OF TWINNING FRACTION: ALPHA=0.50(05). REFINEMENT WITH IDEALISED HYDROGEN ATOMS TWINNED DATA; APPARENT SYMMETRY I422; TWINNING OPERATOR
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 695 5.2 %13457
all0.2671 ---
obs0.2658 -94.4 %-
Refinement stepCycle: LAST / Resolution: 2→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 0 68 1835
Refinement
*PLUS
Rfactor all: 0.21 / Rfactor obs: 0.252 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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