[English] 日本語
Yorodumi
- PDB-2rig: CRYSTAL STRUCTURE OF RECOMBINANT RABBIT INTERFERON-GAMMA AT 2.7-A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rig
TitleCRYSTAL STRUCTURE OF RECOMBINANT RABBIT INTERFERON-GAMMA AT 2.7-ANGSTROMS RESOLUTION
ComponentsINTERFERON-GAMMA
KeywordsCYTOKINE
Function / homology
Function and homology information


type II interferon receptor binding / humoral immune response / positive regulation of autophagy / cytokine activity / defense response to virus / adaptive immune response / extracellular space
Similarity search - Function
Interferon gamma / Interferon gamma / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSamudzi, C.T. / Burton, L.E. / Rubin, J.R.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: Crystal structure of recombinant rabbit interferon-gamma at 2.7-A resolution.
Authors: Samudzi, C.T. / Burton, L.E. / Rubin, J.R.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1991
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Recombinant Rabbit Interferon-Gamma
Authors: Samudzi, C.T. / Gribskov, C.L. / Burton, L.E. / Rubin, J.R.
History
DepositionJan 11, 1993Processing site: BNL
SupersessionJan 15, 1993ID: 1RIG
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INTERFERON-GAMMA


Theoretical massNumber of molelcules
Total (without water)16,9501
Polymers16,9501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.713, 57.713, 177.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein INTERFERON-GAMMA / Coordinate model: Cα atoms only


Mass: 16950.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P30123

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
2100 mMTris-HCl11
33.2 M11NaCl

-
Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 3284 / % possible obs: 84 % / Observed criterion σ(I): 2 / Num. measured all: 21224 / Rmerge(I) obs: 0.058

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.212 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms119 0 0 0 119
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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