[English] 日本語
Yorodumi
- PDB-2ojz: Anti-DNA antibody ED10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ojz
TitleAnti-DNA antibody ED10
Components
  • Fab ED10 heavy chain
  • Fab ED10 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / immune response / extracellular space / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mc5 VHCH1 / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsStanfield, R.L. / Sanguineti, S. / Wilson, I.A. / de Prat-Gay, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Specific recognition of a DNA immunogen by its elicited antibody
Authors: Sanguineti, S. / Centeno Crowley, J.M. / Lodeiro Merlo, M.F. / Cerutti, M.L. / Wilson, I.A. / Goldbaum, F.A. / Stanfield, R.L. / de Prat-Gay, G.
History
DepositionJan 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE Currently, there is no aminoacid database reference available for the proteins

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab ED10 light chain
H: Fab ED10 heavy chain
M: Fab ED10 light chain
I: Fab ED10 heavy chain


Theoretical massNumber of molelcules
Total (without water)95,2804
Polymers95,2804
Non-polymers00
Water36020
1
L: Fab ED10 light chain
H: Fab ED10 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-22 kcal/mol
Surface area19760 Å2
MethodPISA
2
M: Fab ED10 light chain
I: Fab ED10 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-23 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.899, 194.045, 61.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21M
12H
22I

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLYSLYS1LA1 - 1071 - 112
221ASPASPLYSLYS1MC1 - 1071 - 112
131ARGARGGLUGLU2LA108 - 213113 - 218
241ARGARGGLUGLU2MC108 - 213113 - 218
112GLUGLUSERSER1HB1 - 1131 - 116
222GLUGLUSERSER1ID1 - 1131 - 116
132ALAALAARGARG2HB114 - 228117 - 216
242ALAALAARGARG2ID114 - 228117 - 216

NCS ensembles :
IDDetails
1L M
2H I

-
Components

#1: Antibody Fab ED10 light chain


Mass: 24148.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS
#2: Antibody Fab ED10 heavy chain


Mass: 23491.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0N7J2*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate, 25% MPEG 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.73→25.4 Å / Num. all: 27701 / Num. obs: 27701 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 47.2 Å2 / Rsym value: 11 / Net I/σ(I): 16
Reflection shellResolution: 2.73→2.8 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2699 / Rsym value: 45.3 / % possible all: 97

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ggi

1ggi


Resolution: 2.73→25.24 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.883 / SU B: 27.962 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26438 1349 4.9 %RANDOM
Rwork0.2012 ---
all0.20423 26314 --
obs0.20423 26314 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--1.03 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.73→25.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6688 0 0 20 6708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226870
X-RAY DIFFRACTIONr_bond_other_d0.0020.024568
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9519370
X-RAY DIFFRACTIONr_angle_other_deg1.093.00311184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1995864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06524.403268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.249151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9541522
X-RAY DIFFRACTIONr_chiral_restr0.1010.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027600
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021346
X-RAY DIFFRACTIONr_nbd_refined0.2160.21118
X-RAY DIFFRACTIONr_nbd_other0.2130.24319
X-RAY DIFFRACTIONr_nbtor_refined0.1970.23264
X-RAY DIFFRACTIONr_nbtor_other0.1020.23910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.26
X-RAY DIFFRACTIONr_mcbond_it0.9961.55341
X-RAY DIFFRACTIONr_mcbond_other0.21.51740
X-RAY DIFFRACTIONr_mcangle_it1.25127048
X-RAY DIFFRACTIONr_scbond_it1.83833058
X-RAY DIFFRACTIONr_scangle_it2.6684.52322
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L2069tight positional0.060.05
2H2138tight positional0.050.05
1L761medium positional0.420.5
2H633medium positional0.360.5
1L2069tight thermal0.130.5
2H2138tight thermal0.110.5
1L761medium thermal0.532
2H633medium thermal0.462
LS refinement shellResolution: 2.732→2.802 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 84 -
Rwork0.371 1619 -
obs-1619 100 %

+
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