[English] 日本語
Yorodumi
- PDB-7n38: Crystal structure of 5-site deamidated variant of human gamma(S)-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n38
TitleCrystal structure of 5-site deamidated variant of human gamma(S)-crystallin
ComponentsGamma-crystallin S
KeywordsSTRUCTURAL PROTEIN / crystallin / human crystallin / gamma(S) crystallin / eye lens protein
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
Similarity search - Function
Beta/Gamma crystallin / : / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsNorton-Baker, B. / Mehrabi, P. / Martin, R.W.
CitationJournal: Structure / Year: 2022
Title: Deamidation of the human eye lens protein gamma S-crystallin accelerates oxidative aging.
Authors: Norton-Baker, B. / Mehrabi, P. / Kwok, A.O. / Roskamp, K.W. / Rocha, M.A. / Sprague-Piercy, M.A. / von Stetten, D. / Miller, R.J.D. / Martin, R.W.
History
DepositionMay 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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-crystallin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1983
Polymers20,9651
Non-polymers2342
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.315, 62.694, 79.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Gamma-crystallin S / Beta-crystallin S / Gamma-S-crystallin


Mass: 20964.559 Da / Num. of mol.: 1 / Mutation: N15D,N54D,Q93E,Q121E,N144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGS, CRYG8 / Production host: Escherichia coli (E. coli) / References: UniProt: P22914
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl2, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.22→39.9 Å / Num. obs: 41328 / % possible obs: 93.52 % / Redundancy: 12.8 % / Biso Wilson estimate: 15.58 Å2 / CC1/2: 1 / Net I/σ(I): 30.24
Reflection shellResolution: 1.22→1.27 Å / Num. unique obs: 2350 / CC1/2: 0.715

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FD8

6fd8


Resolution: 1.22→39.9 Å / SU ML: 0.1098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6966
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1792 2077 5.03 %
Rwork0.1464 39247 -
obs0.148 41324 93.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.92 Å2
Refinement stepCycle: LAST / Resolution: 1.22→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 15 227 1684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971662
X-RAY DIFFRACTIONf_angle_d1.08222268
X-RAY DIFFRACTIONf_chiral_restr0.1085215
X-RAY DIFFRACTIONf_plane_restr0.0076304
X-RAY DIFFRACTIONf_dihedral_angle_d25.617651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.3605520.23321090X-RAY DIFFRACTION39.57
1.25-1.280.23521120.20432362X-RAY DIFFRACTION85.28
1.28-1.320.2711350.18722675X-RAY DIFFRACTION96.63
1.32-1.360.18571440.16612663X-RAY DIFFRACTION97.2
1.36-1.40.19891560.15472681X-RAY DIFFRACTION97.12
1.4-1.450.21211560.13922673X-RAY DIFFRACTION97.32
1.45-1.510.19231310.13042701X-RAY DIFFRACTION97.55
1.51-1.580.15181470.12632735X-RAY DIFFRACTION98.19
1.58-1.660.15651400.12242733X-RAY DIFFRACTION98.36
1.66-1.770.20111390.13512753X-RAY DIFFRACTION98.6
1.77-1.90.16661320.13642764X-RAY DIFFRACTION98.3
1.9-2.090.16981440.13752814X-RAY DIFFRACTION98.7
2.09-2.40.16471640.13912774X-RAY DIFFRACTION99.56
2.4-3.020.18231760.1622843X-RAY DIFFRACTION99.87
3.02-39.90.17671490.14612986X-RAY DIFFRACTION98.99

+
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