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Yorodumi- EMDB-26161: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26161 | |||||||||
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Title | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg) | |||||||||
Map data | Locally filtered map used for refinement. | |||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Sharon I / Grogg M / Hilvert D / Schmeing TM | |||||||||
Funding support | Canada, 1 items
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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 TM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26161.map.gz | 11 MB | EMDB map data format | |
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Header (meta data) | emd-26161-v30.xml emd-26161.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26161_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_26161.png | 51.8 KB | ||
Masks | emd_26161_msk_1.map | 244.1 MB | Mask map | |
Others | emd_26161_additional_1.map.gz emd_26161_half_map_1.map.gz emd_26161_half_map_2.map.gz | 230 MB 226.1 MB 226.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26161 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26161 | HTTPS FTP |
-Validation report
Summary document | emd_26161_validation.pdf.gz | 775.8 KB | Display | EMDB validaton report |
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Full document | emd_26161_full_validation.pdf.gz | 775.3 KB | Display | |
Data in XML | emd_26161_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_26161_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26161 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26161 | HTTPS FTP |
-Related structure data
Related structure data | 7txvMC 7txuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26161.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Locally filtered map used for refinement. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26161_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map before local filtering. Not used for refinement.
File | emd_26161_additional_1.map | ||||||||||||
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Annotation | Sharpened map before local filtering. Not used for refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_26161_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_26161_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit...
Entire | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg) |
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Components |
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-Supramolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit...
Supramolecule | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg) type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Synechocystis sp. PCC 6714 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Experimental: 383 kDa/nm |
-Macromolecule #1: Cyanophycin synthase
Macromolecule | Name: Cyanophycin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: cyanophycin synthase (L-aspartate-adding) |
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Source (natural) | Organism: Synechocystis sp. PCC 6714 (bacteria) / Strain: PCC 6714 |
Molecular weight | Theoretical: 95.757852 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VQHVALELQ ELVGMTAGFG RTRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA N SALGPSTE ...String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VQHVALELQ ELVGMTAGFG RTRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA N SALGPSTE TIVTEAEARK IPWMLLSARA MVQLGYGVYQ QRIQATLSSH SGILGVELAC DKEGTKTILQ DAGIPVPRGT TI QYFDDLE EAINDVGGYP VVIKPLDGNH GRGITINVRH WQEAIAAYDL AAEESKSRAI IVERYYEGSD HRVLVVNGKL VAV AERIPA HVTGDGSSTI SELIEKTNQD PNRGDGHDNI LTKIVVNKTA IDVMERQGYN LDSVLPKDEV VYLRATANLS TGGI AIDRT DDIHPENIWL MERVAKVIGL DIAGIDVVTS DISKPLRETN GVIVEVNAAP GFRMHVAPSQ GLPRNVAAPV LDMLF PPGT PSRIPILAVT GTNGKTTTTR LLAHIYRQTG KTVGYTSTDA IYINEYCVEK GDNTGPQSAG VILRDPTVEV AVLETA RGG ILRAGLAFDS CDVGVVLNVA ADHLGLGDID TIEQMAKVKS VIAEVVDPSG YAVLNADDPL VAAMADKVKA KVAYFSM NP DNPIIQAHVR RNGIAAVYES GYLSILEGSW TLRVEQAKLI PMTMGGMAPF MIANALAACL AAFVNGLDVE VIRQGVRT F TTSAEQTPGR MNLFNLGQHH ALVDYAHNPA GYRAVGDFVK NWQGQRFGVV GGPGDRRDSD LIELGQIAAQ VFDRIIVKE DDDKRGRSEG ETADLIVKGI LQENPGASYE VILDETIALN KALDQVEEKG LVVVFPESVT RAIDLIKVRN PIGENLYFQ |
-Macromolecule #2: 16x(Asp-Arg)
Macromolecule | Name: 16x(Asp-Arg) / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.35838 KDa |
Sequence | String: (7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID) (7ID)(7ID)(7ID)(7ID)(7ID)(7ID) |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |