[English] 日本語
Yorodumi
- PDB-9udr: Single-chain Fv antibody of B2 complex with NP-glycine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9udr
TitleSingle-chain Fv antibody of B2 complex with NP-glycine
ComponentsSingle-chain Fv antibody of B2
KeywordsIMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION
Function / homology:
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsYoshida, M. / Hanazono, Y. / Numoto, N. / Ito, N. / Oda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch.Biochem.Biophys. / Year: 2026
Title: Structural basis of affinity maturation of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies.
Authors: Yoshida, M. / Hanazono, Y. / Numoto, N. / Yabuno, S. / Ito, N. / Azuma, T. / Oda, M.
History
DepositionApr 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2026Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / chem_comp_bond ...chem_comp / chem_comp_bond / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp_bond.value_order ..._chem_comp.name / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Apr 22, 2026Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-chain Fv antibody of B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0582
Polymers25,8041
Non-polymers2541
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.039, 71.834, 82.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Antibody Single-chain Fv antibody of B2


Mass: 25803.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-A1LZO / N-[(4-hydroxy-3-nitrophenyl)acetyl]glycine


Mass: 254.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BICINE pH 9.0, 2% v/v 1,4-dioxane, 10% w/v polyethylene glycol 20,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 53602 / % possible obs: 99.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 11.95 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20
Reflection shellResolution: 1.34→1.36 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2443 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→41.03 Å / SU ML: 0.1018 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.3413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1632 2677 5 %
Rwork0.1506 50849 -
obs0.1512 53526 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.61 Å2
Refinement stepCycle: LAST / Resolution: 1.34→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 18 279 2050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01342028
X-RAY DIFFRACTIONf_angle_d1.26832793
X-RAY DIFFRACTIONf_chiral_restr0.1095303
X-RAY DIFFRACTIONf_plane_restr0.0095365
X-RAY DIFFRACTIONf_dihedral_angle_d14.6381744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.23361300.2442466X-RAY DIFFRACTION92.65
1.36-1.390.21911320.21332508X-RAY DIFFRACTION94.9
1.39-1.420.19011390.19242634X-RAY DIFFRACTION98.82
1.42-1.450.20761390.17542657X-RAY DIFFRACTION99.96
1.45-1.480.19071400.16452665X-RAY DIFFRACTION99.96
1.48-1.520.19531410.15582674X-RAY DIFFRACTION100
1.52-1.560.17191400.14772642X-RAY DIFFRACTION99.93
1.56-1.610.17281420.14822705X-RAY DIFFRACTION100
1.61-1.660.17911390.14322659X-RAY DIFFRACTION99.93
1.66-1.720.15811400.15032660X-RAY DIFFRACTION99.89
1.72-1.790.15151420.15042690X-RAY DIFFRACTION99.89
1.79-1.870.14921410.14782686X-RAY DIFFRACTION99.96
1.87-1.970.14461420.1422676X-RAY DIFFRACTION99.93
1.97-2.090.15481420.13462705X-RAY DIFFRACTION100
2.09-2.250.18751420.14332703X-RAY DIFFRACTION100
2.25-2.480.14611440.14822731X-RAY DIFFRACTION99.9
2.48-2.840.16921440.15172730X-RAY DIFFRACTION99.9
2.84-3.570.15151450.14492766X-RAY DIFFRACTION99.9
3.58-41.030.15071530.1462892X-RAY DIFFRACTION99.48
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3933449582740.1752443955560.0200631693670.4258787415670.346144854570.8556944628010.01899237111730.00862008695568-0.0349717647006-0.0313051126321-0.007948863811830.0130800926583-0.04153062967950.02179271307640.0003149449569210.09141913013840.00490866192117-0.001552548804960.09046815157970.0002632791164610.091518784894515.05160857728.876767572824.3977884613
20.519168455151-0.340265934391-0.166097835880.9751049683080.3056417570771.00097345062-0.0471575069481-0.014751197816-0.02004477794080.0487279011206-0.006844898092980.03887548786860.0671572841-0.0270481367223-0.09532436262460.0815978101822-0.01017801483850.006525389524080.087202906393-0.00453044373560.090013987459113.3042982507-6.8476227057210.5244888135
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 113 )2 - 1131 - 112
22chain 'A' and (resid 128 through 245 )128 - 245113 - 230

+
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://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