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- EMDB-26161: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-26161
TitleCyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)
Map dataLocally filtered map used for refinement.
Sample
  • Complex: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)
    • Protein or peptide: Cyanophycin synthase
  • Protein or peptide: 16x(Asp-Arg)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCyanophycin / CphA1 / ATP-grasp / enzyme / LIGASE
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) / biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Cyanophycin synthetase / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily ...Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Cyanophycin synthetase / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
Cyanophycin synthetase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6714 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSharon I / Grogg M
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)178084 Canada
CitationJournal: 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
DepositionFeb 9, 2022-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26161.png

Downloads & links

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Map

FileDownload / File: emd_26161.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally filtered map used for refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å		0.86 Å/pix.
x 400 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.59
Minimum - Maximum-3.2029445 - 5.385246
Average (Standard dev.)0.0053728516 (±0.102711305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26161_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map before local filtering. Not used for refinement.

Fileemd_26161_additional_1.map
AnnotationSharpened map before local filtering. Not used for refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_26161_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_26161_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit...

EntireName: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)
Components
  • Complex: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)
    • Protein or peptide: Cyanophycin synthase
  • Protein or peptide: 16x(Asp-Arg)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q wit...

SupramoleculeName: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
Molecular weightTheoretical: 383 kDa/nm

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Macromolecule #1: Cyanophycin synthase

MacromoleculeName: Cyanophycin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: cyanophycin synthase (L-aspartate-adding)
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria) / Strain: PCC 6714
Molecular weightTheoretical: 95.757852 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

UniProtKB: Cyanophycin synthetase

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Macromolecule #2: 16x(Asp-Arg)

MacromoleculeName: 16x(Asp-Arg) / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.35838 KDa
SequenceString:
(7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID)(7ID) (7ID)(7ID)(7ID)(7ID)(7ID)(7ID)

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lg5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 318594
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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