[English] 日本語
Yorodumi
- PDB-7ta5: Crystal structure of cyanophycin synthetase 2 from Gloeothece cit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ta5
TitleCrystal structure of cyanophycin synthetase 2 from Gloeothece citriformis
ComponentsGlutathione synthase
KeywordsLIGASE / cyanophycin / ATP-grasp / CphA
Function / homology
Function and homology information


glutathione synthase / ribosomal S6-glutamic acid ligase activity / glutathione synthase activity / SOS response / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Glutathione synthase
Similarity search - Component
Biological speciesGloeothece citriformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSharon, I. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)178084 Canada
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structure and Function of the beta-Asp-Arg Polymerase Cyanophycin Synthetase 2.
Authors: Sharon, I. / Grogg, M. / Hilvert, D. / Schmeing, T.M.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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: Glutathione synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2885
Polymers71,7031
Non-polymers5854
Water19811
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)99.781, 99.781, 348.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Glutathione synthase


Mass: 71702.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeothece citriformis (bacteria) / Strain: PCC 7424 / Gene: PCC7424_0612 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7KEP8, glutathione synthase
#2: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: tris-bicine pH8.5 200mM Na/K tartrate 60mM MgCl 10mM betaine 44% precip 2 4% 2,2,2-trifluoroethanol 10mM NiCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5213 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5213 Å / Relative weight: 1
ReflectionResolution: 3→348.5 Å / Num. obs: 21675 / % possible obs: 100 % / Redundancy: 105 % / CC1/2: 0.998 / Rmerge(I) obs: 0.47 / Net I/σ(I): 18.3
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 5.649 / Num. unique obs: 3378 / CC1/2: 0.451

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2-4158_final: ???)refinement
DIALSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LGJ

7lgj


Resolution: 3→116.16 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 31.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 1106 5.12 %
Rwork0.2639 --
obs0.265 21583 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→116.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 39 11 4746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094839
X-RAY DIFFRACTIONf_angle_d1.666570
X-RAY DIFFRACTIONf_dihedral_angle_d12.0631788
X-RAY DIFFRACTIONf_chiral_restr0.093733
X-RAY DIFFRACTIONf_plane_restr0.007846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.43411300.41022483X-RAY DIFFRACTION100
3.14-3.30.41821500.37962459X-RAY DIFFRACTION100
3.3-3.510.33351320.32572500X-RAY DIFFRACTION100
3.51-3.780.27471290.27172532X-RAY DIFFRACTION100
3.78-4.160.29511280.25922542X-RAY DIFFRACTION100
4.16-4.760.27271360.222550X-RAY DIFFRACTION100
4.76-60.28041540.22952591X-RAY DIFFRACTION100
6-116.160.22581470.2372820X-RAY DIFFRACTION100

+
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