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- PDB-1oaz: IgE Fv SPE7 complexed with a recombinant thioredoxin -

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Basic information

Entry
Database: PDB / ID: 1oaz
TitleIgE Fv SPE7 complexed with a recombinant thioredoxin
Components
  • (IMMUNOGLOBULIN E) x 2
  • THIOREDOXIN 1
KeywordsIMMUNE SYSTEM / ANTIBODY-COMPLEX / ANTIBODY / ALLERGY / IGE / CONFORMATIONAL DIVERSITY / MULTISPECFICITY / REDOX-ACTIVE CENTER / ELECTRON TRANSPORT
Function / homology
Function and homology information


positive regulation of DNA-directed DNA polymerase activity / DNA polymerase processivity factor activity / immunoglobulin complex / protein-disulfide reductase activity / cell redox homeostasis / adaptive immune response / oxidoreductase activity / immune response / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / : / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Glutaredoxin ...Thioredoxin / Thioredoxin / : / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Glutaredoxin / Immunoglobulin V-set domain / Glutaredoxin / Immunoglobulin subtype / Immunoglobulin / Thioredoxin-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Thioredoxin 1 / Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104 / Thioredoxin 1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 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 / 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 / _pdbx_database_status.status_code_sf
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
A: THIOREDOXIN 1
B: THIOREDOXIN 1
H: IMMUNOGLOBULIN E
J: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E
N: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)77,3696
Polymers77,3696
Non-polymers00
Water6,503361
1
A: THIOREDOXIN 1
H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)38,6843
Polymers38,6843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-28.7 kcal/mol
Surface area19100 Å2
MethodPQS
2
B: THIOREDOXIN 1
J: IMMUNOGLOBULIN E
N: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)38,6843
Polymers38,6843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-29 kcal/mol
Surface area19040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.352, 79.467, 170.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21N
12H
22J
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111L1 - 22
2111N1 - 22
1211L37 - 48
2211N37 - 48
1311L61 - 84
2311N61 - 84
1411L96 - 101
2411N96 - 101
1121H1 - 23
2121J1 - 23
1221H37 - 49
2221J37 - 49
1321H66 - 94
2321J66 - 94
1421H108 - 122
2421J108 - 122
1131A2 - 100
2131B2 - 100

NCS ensembles :
ID
1
2
3

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

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Components

#1: Protein THIOREDOXIN 1 / TRX1 / TRX / TRXA / TSNC / FIPA


Mass: 13466.326 Da / Num. of mol.: 2 / Fragment: TRX-SHEAR3, RESIDUES 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: EXPRESSED AS RECOMBINANT IN E.COLI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG.1 / References: UniProt: P00274, UniProt: P0AA25*PLUS
#2: Antibody IMMUNOGLOBULIN E


Mass: 13687.315 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)
#3: Antibody IMMUNOGLOBULIN E


Mass: 11530.808 Da / Num. of mol.: 2 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 5
Details: 21% PEG 8K, 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.00
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
128.5 %PEG40001reservoir
20.1 Mmagnesium acetate1reservoir
30.1 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoirpH6.5

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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: 2.25→35.8 Å / Num. obs: 26942 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.067
Reflection shellRmerge(I) obs: 0.114
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 27717 / % possible obs: 99.2 % / Redundancy: 11 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANQ

1anq


Resolution: 2.78→30.15 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.85 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1393 5 %RANDOM
Rwork0.208 ---
obs-26324 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 53.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--1.6 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.78→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5278 0 0 361 5639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0215402
X-RAY DIFFRACTIONr_bond_other_d0.0020.024776
X-RAY DIFFRACTIONr_angle_refined_deg2.371.9497344
X-RAY DIFFRACTIONr_angle_other_deg1.338311140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4355682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026012
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021078
X-RAY DIFFRACTIONr_nbd_refined0.2660.21496
X-RAY DIFFRACTIONr_nbd_other0.2780.26414
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1030.23319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3731.53404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.57625456
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.47231998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.814.51888
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L886tight positional0.050.05
2H1133tight positional0.020.05
3A1390tight positional0.010.05
1L886tight thermal0.050.5
2H1133tight thermal0.050.5
3A1390tight thermal0.010.5
LS refinement shellResolution: 2.78→2.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.368 102
Rwork0.269 1830
Refinement
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / Rfactor Rwork: 0.201

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