[English] 日本語
Yorodumi
- PDB-8iqr: Crystal structure of Anti-PEG antibody M9 Fv-clasp fragment with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iqr
TitleCrystal structure of Anti-PEG antibody M9 Fv-clasp fragment with PEG (co-crystallization with PEG550DME)
Components
  • M9 VH-SARAH
  • M9 VL-SARAH
KeywordsIMMUNE SYSTEM
Function / homology:
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMori, T. / Teramoto, T. / Liu, Y. / Mori, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Comparation of structures and binding properties between two anti-polyethylene glycol antibodies induced via T cell-independent and T cell-dependent pathway
Authors: Liu, Y. / Mori, T. / Teramoto, T. / Kakuta, Y. / Mori, T.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: M9 VL-SARAH
H: M9 VH-SARAH
l: M9 VL-SARAH
h: M9 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2266
Polymers82,4014
Non-polymers8252
Water2,270126
1
L: M9 VL-SARAH
H: M9 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6133
Polymers41,2012
Non-polymers4131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-44 kcal/mol
Surface area16760 Å2
MethodPISA
2
l: M9 VL-SARAH
h: M9 VH-SARAH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6133
Polymers41,2012
Non-polymers4131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-42 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.100, 82.780, 71.170
Angle α, β, γ (deg.)90.00, 117.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody M9 VL-SARAH


Mass: 20273.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MSKIKGHHHHHHGG is derived from plasmid. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody M9 VH-SARAH


Mass: 20927.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MSKIKGHHHHHHGG is derived from plasmid. / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-HZA / 2,5,8,11,14,17,20,23,26-nonaoxaoctacosane


Mass: 412.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C19H40O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.42 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium formate and 16% (v/v) PEG 550DME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→49.4 Å / Num. obs: 29444 / % possible obs: 98.2 % / Redundancy: 3.18 % / CC1/2: 0.997 / Rrim(I) all: 0.108 / Net I/σ(I): 10.36
Reflection shellResolution: 2.35→2.49 Å / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4683 / CC1/2: 0.572 / Rrim(I) all: 1.062

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→49.4 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2921 2021 6.87 %
Rwork0.2353 --
obs0.2391 29403 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 53 126 5410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025393
X-RAY DIFFRACTIONf_angle_d0.4687264
X-RAY DIFFRACTIONf_dihedral_angle_d19.3442017
X-RAY DIFFRACTIONf_chiral_restr0.039777
X-RAY DIFFRACTIONf_plane_restr0.003918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.33881440.3281930X-RAY DIFFRACTION99
2.41-2.470.34581520.32561961X-RAY DIFFRACTION99
2.47-2.550.4291440.3261975X-RAY DIFFRACTION99
2.55-2.630.35691410.32631967X-RAY DIFFRACTION99
2.63-2.720.37681490.30531937X-RAY DIFFRACTION99
2.72-2.830.34631350.30291964X-RAY DIFFRACTION99
2.83-2.960.32631460.27641956X-RAY DIFFRACTION99
2.96-3.120.34681420.27911953X-RAY DIFFRACTION99
3.12-3.310.30031520.26221966X-RAY DIFFRACTION98
3.31-3.570.28771450.23781954X-RAY DIFFRACTION99
3.57-3.930.31051470.22641955X-RAY DIFFRACTION98
3.93-4.490.24761370.19621940X-RAY DIFFRACTION97
4.49-5.660.24761550.18671944X-RAY DIFFRACTION97
5.66-49.40.23811320.19091980X-RAY DIFFRACTION96

+
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