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- PDB-1oax: Fv Structure of the IgE SPE-7 in complex with acenaphthenequinone -

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Basic information

Entry
Database: PDB / ID: 1oax
TitleFv Structure of the IgE SPE-7 in complex with acenaphthenequinone
Components(IMMUNOGLOBULIN E) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY-COMPLEX / ANTIBODY / ALLERGY / IGE
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
ACENAPHTHENEQUINONE / 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: 2.67 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 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)73,9998
Polymers73,6346
Non-polymers3642
Water1,26170
1
H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4263
Polymers25,2442
Non-polymers1821
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)25,4263
Polymers25,2442
Non-polymers1821
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)78.726, 78.636, 167.564
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
11H
21J
12L
22N
13M
23O
44

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111H3 - 115
2111J3 - 115
1121L3 - 110
2121N3 - 110
1131M6 - 109
2131O6 - 109

NCS ensembles :
ID
1
2
3
4

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-ANQ / ACENAPHTHENEQUINONE


Mass: 182.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 5.5
Details: 21% PEG 8K 0.1M NA CACODYLATE, 0.2M NA ACETATE PH5.5, pH 5.50

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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: Oct 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: 2.66→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 shellResolution: 2.67→2.98 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.6 / % possible all: 91.7

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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: 2.67→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.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1532 5.1 %RANDOM
Rwork0.238 ---
obs-28729 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: 40.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.67→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 28 70 5206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.2070.0215467
X-RAY DIFFRACTIONr_bond_other_d0.0210.024756
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg6.5291.9377452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.875311049
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_restr13.5855688
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.026114
X-RAY DIFFRACTIONr_gen_planes_other0.0240.021160
X-RAY DIFFRACTIONr_nbd_refined0.510.21445
X-RAY DIFFRACTIONr_nbd_other0.3550.25987
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1360.23597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4270.2189
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3650.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6130.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4471.53429
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.12325498
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.16732038
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.0844.51954
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11H1686tight positional0.060.05
21L1519tight positional0.050.05
44M1455tight positional0.160.05
11H1686tight thermal0.260.5
21L1519tight thermal0.270.5
44M1455tight thermal0.20.5
LS refinement shellResolution: 2.67→2.73 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 92
Rwork0.298 1987

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