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- PDB-1oar: Fv IgE SPE-7 in complex with Alizarin Red -

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Basic information

Entry
Database: PDB / ID: 1oar
TitleFv IgE SPE-7 in complex with Alizarin Red
Components
  • IMMUNOGLOBULIN E
  • IMMUNOGLOBULING E
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
ALIZARIN RED / CACODYLATE ION / 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: 2.23 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 / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
I: IMMUNOGLOBULIN E
J: IMMUNOGLOBULIN E
K: IMMUNOGLOBULIN E
L: IMMUNOGLOBULING E
M: IMMUNOGLOBULING E
N: IMMUNOGLOBULING E
O: IMMUNOGLOBULING E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,84854
Polymers100,8728
Non-polymers3,97646
Water6,341352
1
H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULING E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,82722
Polymers25,2182
Non-polymers1,60920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-60 kcal/mol
Surface area10800 Å2
MethodPQS
2
I: IMMUNOGLOBULIN E
M: IMMUNOGLOBULING E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6206
Polymers25,2182
Non-polymers4024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-16.9 kcal/mol
Surface area11160 Å2
MethodPQS
3
J: IMMUNOGLOBULIN E
N: IMMUNOGLOBULING E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,82722
Polymers25,2182
Non-polymers1,60920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-73.7 kcal/mol
Surface area10750 Å2
MethodPQS
4
K: IMMUNOGLOBULIN E
O: IMMUNOGLOBULING E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5744
Polymers25,2182
Non-polymers3562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-17 kcal/mol
Surface area11080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.917, 78.882, 169.036
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

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Antibody , 2 types, 8 molecules HIJKLMNO

#1: Antibody
IMMUNOGLOBULIN E


Mass: 13687.315 Da / Num. of mol.: 4 / Fragment: FV, 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
IMMUNOGLOBULING E


Mass: 11530.808 Da / Num. of mol.: 4 / Fragment: FV, RESIDUES 1-110
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

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Non-polymers , 7 types, 398 molecules

#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-AZN / ALIZARIN RED


Mass: 320.274 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H8O7S
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
121 %PEG80001reservoir
20.1 Msodium cacodylate1reservoir
30.2 Msodium acetate1reservoirpH5.5

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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: 2.2 Å / Num. obs: 52239 / Redundancy: 13.7 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANQ

1anq


Resolution: 2.23→33.71 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.653 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2666 5.1 %RANDOM
Rwork0.205 ---
obs-49572 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: 52.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.23→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 216 352 7050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.2070.0216738
X-RAY DIFFRACTIONr_bond_other_d0.0920.025971
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg3.9951.949104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2.142313816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr7.4645815
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.027288
X-RAY DIFFRACTIONr_gen_planes_other0.0160.021414
X-RAY DIFFRACTIONr_nbd_refined0.6320.21712
X-RAY DIFFRACTIONr_nbd_other0.370.27568
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.120.24043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.249
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3790.2175
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3080.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1721.54136
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.53526618
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.02432602
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1364.52486
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
LS refinement shellResolution: 2.23→2.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 195
Rwork0.201 3404
Refinement
*PLUS
Highest resolution: 2.2 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.209

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