[English] 日本語
Yorodumi
- PDB-7d9m: grass carp interleukin-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d9m
Titlegrass carp interleukin-2
ComponentsInterleukin
KeywordsCYTOKINE / interleukin-2 / fish / grass carp
Function / homologyInterleukin-15/Interleukin-21 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha / Interleukin-2
Function and homology information
Biological speciesCtenopharyngodon idella (grass carp)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.66 Å
AuthorsJunya, w. / Jun, z.
CitationJournal: Dev.Comp.Immunol. / Year: 2020
Title: Structural insights into the co-evolution of IL-2 and its private receptor in fish.
Authors: Wang, J. / Wang, W. / Xu, J. / Jia, Z. / Liu, Q. / Zhu, X. / Xia, C. / Zou, J.
History
DepositionOct 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Interleukin
D: Interleukin


Theoretical massNumber of molelcules
Total (without water)27,9762
Polymers27,9762
Non-polymers00
Water00
1
B: Interleukin

D: Interleukin


Theoretical massNumber of molelcules
Total (without water)27,9762
Polymers27,9762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/61
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.090, 83.090, 302.931
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

-
Components

#1: Protein Interleukin


Mass: 13987.960 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Gene: IL-2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4D6NYT7
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.4 Å3/Da / Density % sol: 77.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.4 M Sodium phosphate monobasic monohydrate, Potassium Phosphate dibasic (pH 8.2)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.66→45 Å / Num. obs: 17766 / % possible obs: 93.1 % / Redundancy: 5.2 % / Biso Wilson estimate: 40.62 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.3
Reflection shellResolution: 2.66→10 Å / Num. unique obs: 8666 / CC1/2: 0.738

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.66→38.42 Å / SU ML: 0.4724 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.5505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.4117 860 4.84 %
Rwork0.3773 16906 -
obs0.3779 17766 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.86 Å2
Refinement stepCycle: LAST / Resolution: 2.66→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 0 1850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01021878
X-RAY DIFFRACTIONf_angle_d1.17462526
X-RAY DIFFRACTIONf_chiral_restr0.0475284
X-RAY DIFFRACTIONf_plane_restr0.0066324
X-RAY DIFFRACTIONf_dihedral_angle_d20.754246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.820.3651900.34611930X-RAY DIFFRACTION66.49
2.82-3.040.39531470.35922893X-RAY DIFFRACTION99.74
3.04-3.350.39721440.37432934X-RAY DIFFRACTION100
3.35-3.830.41811430.35582943X-RAY DIFFRACTION99.68
3.83-4.830.41151600.35283005X-RAY DIFFRACTION99.91
4.83-38.420.42821760.42773201X-RAY DIFFRACTION99.53

+
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