[English] 日本語
Yorodumi
- PDB-4gcr: STRUCTURE OF THE BOVINE EYE LENS PROTEIN GAMMA-B (GAMMA-II)-CRYST... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gcr
TitleSTRUCTURE OF THE BOVINE EYE LENS PROTEIN GAMMA-B (GAMMA-II)-CRYSTALLIN AT 1.47 ANGSTROMS
ComponentsGAMMA-B CRYSTALLIN
KeywordsEYE LENS PROTEIN
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
Similarity search - Function
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.47 Å
AuthorsSlingsby, C. / Najmudin, S. / Nalini, V. / Driessen, H.P.C. / Blundell, T.L. / Moss, D.S. / Lindley, P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of the bovine eye lens protein gammaB(gammaII)-crystallin at 1.47 A.
Authors: Najmudin, S. / Nalini, V. / Driessen, H.P. / Slingsby, C. / Blundell, T.L. / Moss, D.S. / Lindley, P.F.
#1: Journal: Pept.Protein Rev. / Year: 1984
Title: X-Ray Studies of the Lens Specific Proteins, the Crystallins
Authors: Summers, L. / Wistow, G. / Narebor, M. / Moss, D. / Lindley, P. / Slingsby, C. / Blundell, T. / Bartunik, H. / Bartels, K.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Gamma-II Crystallin at 1.9 Angstrom Resolution
Authors: Wistow, G. / Turnell, B. / Summers, L. / Slingsby, C. / Moss, D. / Miller, L. / Lindley, P. / Blundell, T.
#3: Journal: Nature / Year: 1981
Title: X-Ray Analysis of Gamma Crystallin II
Authors: Blundell, T. / Lindley, P. / Miller, L. / Moss, D. / Slingsby, C. / Tickle, I. / Turnell, B. / Wistow, G.
History
DepositionApr 2, 1992Processing site: BNL
SupersessionOct 15, 1993ID: 1GCR
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GAMMA-B CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)20,9931
Polymers20,9931
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.530, 57.530, 97.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein GAMMA-B CRYSTALLIN


Mass: 20992.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P02526
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A BETA-BRIDGE BETWEEN RESIDUES 119 - 121 AND 162 - 164.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal grow
*PLUS
Temperature: 0 K / pH: 7 / Method: unknown / Details: Carlisle, C.H.,(1977) J. Mol. Biol., 110, 417.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
170 mg/mlprotein11
20.05 Mphosphate12
31 mMdithiothreitol12

-
Data collection

Reflection
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 9999 Å / Num. obs: 26151 / Rmerge(I) obs: 0.084 / Num. measured all: 118540

-
Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.181 / Highest resolution: 1.47 Å
Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR COLUMN OF THE ATOM AND HETATM RECORDS BELOW IS UISO (U**2), WHICH IS THE MEAN-SQUARE AMPLITUDE VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR COLUMN OF THE ATOM AND HETATM RECORDS BELOW IS UISO (U**2), WHICH IS THE MEAN-SQUARE AMPLITUDE VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE RELATION: B = 8*(PI)**2*U**2.
Refinement stepCycle: LAST / Highest resolution: 1.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 0 230 1786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.038
Refinement
*PLUS
Highest resolution: 1.47 Å / Lowest resolution: 8 Å / Rfactor obs: 0.181 / Num. reflection obs: 29773
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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