[English] 日本語
Yorodumi
- PDB-1oau: Fv Structure of the IgE SPE-7 in complex with DNP-Ser (immunising... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oau
TitleFv Structure of the IgE SPE-7 in complex with DNP-Ser (immunising hapten)
Components(IMMUNOGLOBULIN ...) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY-COMPLEX / ANTIBODY / ALLERGY / IGE / CONFORMATIONAL DIVERSITY / MULTISPECIFICITY
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space
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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2,4-DINITROPHENOL / IMIDAZOLE / SERINE / 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: 1.8 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
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: IMMUNOGLOBULIN E
I: IMMUNOGLOBULIN E
J: IMMUNOGLOBULIN E
K: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E
M: IMMUNOGLOBULIN E
N: IMMUNOGLOBULIN E
O: IMMUNOGLOBULIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,58914
Polymers100,8728
Non-polymers7176
Water7,116395
1
H: IMMUNOGLOBULIN E
L: IMMUNOGLOBULIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5765
Polymers25,2182
Non-polymers3583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-19.5 kcal/mol
Surface area12460 Å2
MethodPQS
2
I: IMMUNOGLOBULIN E
M: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)25,2182
Polymers25,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-3.6 kcal/mol
Surface area9870 Å2
MethodPQS
3
J: IMMUNOGLOBULIN E
N: IMMUNOGLOBULIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5765
Polymers25,2182
Non-polymers3583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-19.5 kcal/mol
Surface area12440 Å2
MethodPQS
4
K: IMMUNOGLOBULIN E
O: IMMUNOGLOBULIN E


Theoretical massNumber of molelcules
Total (without water)25,2182
Polymers25,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-4.6 kcal/mol
Surface area9820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.459, 79.480, 168.906
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

-
Components

-
Antibody , 2 types, 8 molecules HIJKLMNO

#1: Antibody
IMMUNOGLOBULIN E


Mass: 13687.315 Da / Num. of mol.: 4 / 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: 11530.808 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

-
Non-polymers , 4 types, 401 molecules

#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Chemical ChemComp-DNF / 2,4-DINITROPHENOL


Mass: 184.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N2O5
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 70 %
Crystal growpH: 7
Details: 24% PEG8K,0.1M NA ACETATE, 0.2M AMMONIUM SULPHATE, PH7, pH 7.00
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %PEG40001reservoir
20.1 Msodium acetate1reservoir
30.2 Mammonium sulfate1reservoirpH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 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: 1.807→30.015 Å / Num. obs: 90268 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.058 / Net I/σ(I): 10.9
Reflection shellResolution: 1.81→1.9 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.399 / % possible all: 70.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 90267 / Redundancy: 3 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 91.4 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANQ

1anq


Resolution: 1.8→30.02 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: 0.071 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 -5.14 %RANDOM
Rwork0.226 ---
obs0.226 90268 91.4 %-
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: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5178 0 48 395 5621
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_deg3.9951.949104
X-RAY DIFFRACTIONr_angle_other_deg2.142313816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4645815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.3615703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr3.0430.21002
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: 1.8→30.02 Å / Total num. of bins used: 20
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.258 / Rfactor Rwork: 0.222

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more