[English] 日本語
Yorodumi
- PDB-6lcs: Crystal structure of 73MuL9 Fv-clasp fragment in complex with GA-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lcs
TitleCrystal structure of 73MuL9 Fv-clasp fragment in complex with GA-pyridine analogue
Components
  • VH-SARAH
  • VL-SARAH
KeywordsIMMUNE SYSTEM / AGE / antibody fragment / fv-clasp
Function / homologyChem-E9R / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNakamura, T. / Takagi, J. / Yamagata, Y. / Morioka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: J.Biochem. / Year: 2021
Title: Molecular recognition of a single-chain Fv antibody specific for GA-pyridine, an advanced glycation end-product (AGE), elucidated using biophysical techniques and synthetic antigen analogues.
Authors: Kobashigawa, Y. / Ohara, T. / Morita, K. / Toyota, Y. / Nakamura, T. / Kotani, S. / Arimori, T. / Yamauchi, S. / Liu, C. / Kitazaki, M. / Wakeyama-Miyazaki, Y. / Suwa, Y. / Uchida-Kamekura, ...Authors: Kobashigawa, Y. / Ohara, T. / Morita, K. / Toyota, Y. / Nakamura, T. / Kotani, S. / Arimori, T. / Yamauchi, S. / Liu, C. / Kitazaki, M. / Wakeyama-Miyazaki, Y. / Suwa, Y. / Uchida-Kamekura, M. / Fukuda, N. / Sato, T. / Nakajima, M. / Takagi, J. / Yamagata, Y. / Morioka, H.
History
DepositionNov 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VH-SARAH
B: VL-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6676
Polymers37,9932
Non-polymers6744
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-54 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.150, 91.150, 119.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Antibody VH-SARAH


Mass: 19952.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The VH domain region (residues 1-113) of this chimeric protein is derived from Mus musculus, while the SARAH domain region (residues 114-164) is derived from Homo sapiens.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody VL-SARAH


Mass: 18040.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The VL domain region (residues 1-108) of this chimeric protein is derived from Mus musculus, while the SARAH domain region (residues 109-159) is derived from Homo sapiens.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-E9R / (2~{S})-6-[4-(hydroxymethyl)-3-oxidanyl-pyridin-1-ium-1-yl]-2-(phenylmethoxycarbonylamino)hexanoic acid


Mass: 389.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium dihydrogen phosphate, dipotassium hydrogenphosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.87 Å / Num. obs: 16107 / % possible obs: 100 % / Redundancy: 25.4 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 32.7
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 1.917 / Num. unique obs: 1155

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XCT

5xct


Resolution: 2.6→43.87 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.96
RfactorNum. reflection% reflection
Rfree0.2597 1508 5.09 %
Rwork0.2137 --
obs0.216 16103 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 36 7 2684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052759
X-RAY DIFFRACTIONf_angle_d0.7723739
X-RAY DIFFRACTIONf_dihedral_angle_d12.1461653
X-RAY DIFFRACTIONf_chiral_restr0.046396
X-RAY DIFFRACTIONf_plane_restr0.004468
LS refinement shellResolution: 2.6001→2.6841 Å
RfactorNum. reflection
Rfree0.3974 139
Rwork0.3707 -
obs-2558

+
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://pdbjlc1.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