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Yorodumi- PDB-7txv: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7txv | ||||||
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Title | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg) | ||||||
Components |
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Keywords | LIGASE / Cyanophycin / CphA1 / ATP-grasp / enzyme | ||||||
Function / homology | Function and homology information cyanophycin synthase (L-aspartate-adding) / cyanophycin synthase (L-arginine-adding) / cyanophycin synthetase activity (L-aspartate-adding) / cyanophycin synthetase activity (L-arginine-adding) / macromolecule biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. PCC 6714 (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Sharon, I. / Grogg, M. / Hilvert, D. / Schmeing, T.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: A cryptic third active site in cyanophycin synthetase creates primers for polymerization Authors: Sharon, I. / Pinus, S. / Grogg, M. / Moitessier, N. / Hilvert, D. / Schmeing, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7txv.cif.gz | 597.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7txv.ent.gz | 503.8 KB | Display | PDB format |
PDBx/mmJSON format | 7txv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7txv_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7txv_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7txv_validation.xml.gz | 113.6 KB | Display | |
Data in CIF | 7txv_validation.cif.gz | 167.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/7txv ftp://data.pdbj.org/pub/pdb/validation_reports/tx/7txv | HTTPS FTP |
-Related structure data
Related structure data | 26161MC 7txuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 95757.852 Da / Num. of mol.: 4 / Mutation: E82Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6714 (bacteria) / Strain: PCC 6714 / Gene: cphA, D082_30240 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A068N621, cyanophycin synthase (L-aspartate-adding), cyanophycin synthase (L-arginine-adding) #2: Protein/peptide | Mass: 4358.380 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-ATP / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg) Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 383 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Synechocystis sp. PCC 6714 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2-4158_final: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 318594 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 2.7 Å | ||||||||||||||||||||||||
Refine LS restraints |
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