[English] 日本語
Yorodumi
- PDB-1i5i: THE C18S MUTANT OF BOVINE (GAMMA-B)-CRYSTALLIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i5i
TitleTHE C18S MUTANT OF BOVINE (GAMMA-B)-CRYSTALLIN
Components(GAMMA-B) CRYSTALLIN
KeywordsSTRUCTURAL PROTEIN / EYE LENS PROTEIN / CRYSTALLIN
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
Similarity search - Function
Crystallins / Beta/Gamma crystallin / Gamma-B Crystallin; domain 1 / 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 (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZarutskie, J.A. / Asherie, N. / Pande, J. / Pande, A. / Lomakin, J. / Lomakin, A. / Ogun, O. / Stern, L.J. / King, J.A. / Benedek, G.B.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Enhanced crystallization of the Cys18 to Ser mutant of bovine gammaB crystallin.
Authors: Asherie, N. / Pande, J. / Pande, A. / Zarutskie, J.A. / Lomakin, J. / Lomakin, A. / Ogun, O. / Stern, L.J. / King, J. / Benedek, G.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of the Bovine Eye Lens Protein Gamma-B (Gamma-II)-Crystallin at 1.47 Angstroms
Authors: Najmudin, S. / Nalini, V. / Driessen, H.P.C. / Slingsby, C. / Blundell, T.L. / Moss, D.S. / Lindley, P.F.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: X-ray analysis of the eye lens protein 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.
#4: Journal: Nature / Year: 1981
Title: The molecular structure and stability of the eye lens: 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
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 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: (GAMMA-B) CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)20,9761
Polymers20,9761
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.850, 57.850, 98.710
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: 20976.494 Da / Num. of mol.: 1 / Mutation: C18S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P02526
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 295 K
Method: chill tube containing protein to 265 k, then bring to 295 k
pH: 7
Details: 100 mM Phosphate, 20 mM DTT, pH 7.0, chill tube containing protein to 265 K, then bring to 295 K

-
Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 26, 1999 / Details: MIRRORS
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 6843 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 21.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 9.6 / Num. unique all: 6843 / Rsym value: 0.146 / % possible all: 92.8

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GCR

4gcr


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: Due to weak electron density in the region of the Tyrosine 174, a good model for the residue could not be refined, and is thus not included in the structure. Density was weak for the CG, SD, ...Details: Due to weak electron density in the region of the Tyrosine 174, a good model for the residue could not be refined, and is thus not included in the structure. Density was weak for the CG, SD, and CE of MET 160 and was not included in the structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 679 10.2 %RANDOM
Rwork0.223 ---
obs-6667 95.3 %-
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 71 1529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d28.6
X-RAY DIFFRACTIONx_improper_angle_d6.6
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 112 10.8 %
Rwork0.242 924 -
obs--92.1 %

+
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