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- PDB-5u6r: E. coli CTP synthase CC mutant filament (product-bound) -

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Basic information

Entry
Database: PDB / ID: 5u6r
TitleE. coli CTP synthase CC mutant filament (product-bound)
ComponentsCTP synthaseCTP synthetase
KeywordsPROTEIN FIBRIL / LIGASE / nucleotide metabolism / metabolic filament
Function / homologyCTP synthase, N-terminal / CTP synthase / Glutamine amidotransferase type 1 domain profile. / CTP synthase N-terminus / Glutamine amidotransferase class-I / CTP synthase GATase domain / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase / Glutamine amidotransferase / CTP synthase ...CTP synthase, N-terminal / CTP synthase / Glutamine amidotransferase type 1 domain profile. / CTP synthase N-terminus / Glutamine amidotransferase class-I / CTP synthase GATase domain / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase / Glutamine amidotransferase / CTP synthase / CTP synthase activity / 'de novo' CTP biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol / CTP synthase / CTP synthase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 5.7 Å resolution
AuthorsKollman, J.M. / Lynch, E.M.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Human CTP synthase filament structure reveals the active enzyme conformation.
Authors: Eric M Lynch / Derrick R Hicks / Matthew Shepherd / James A Endrizzi / Allison Maker / Jesse M Hansen / Rachael M Barry / Zemer Gitai / Enoch P Baldwin / Justin M Kollman
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 8, 2016 / Release: Apr 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 26, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references
1.2Jun 21, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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Assembly

Deposited unit
A: CTP synthase
B: CTP synthase
C: CTP synthase
D: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,42912
Polyers241,7884
Non-polymers3,6418
Water0
1
A: CTP synthase
B: CTP synthase
C: CTP synthase
D: CTP synthase
hetero molecules
x 7


Theoretical massNumber of molelcules
Total (without water)1,718,00584
Polyers1,692,51528
Non-polymers25,49056
Water0
TypeNameSymmetry operationNumber
helical symmetry operation7
2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 7 / Rise per n subunits: 81.591 Å / Rotation per n subunits: 48.563 deg.

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Components

#1: Protein/peptide
CTP synthase / CTP synthetase / Cytidine 5'-triphosphate synthase / Cytidine triphosphate synthetase / CTPS / UTP--ammonia ligase


Mass: 60446.980 Da / Num. of mol.: 4 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrG, ECS88_3048 / Production host: Escherichia coli (E. coli)
References: UniProt: B7MLA1, UniProt: P0A7E5*PLUS, CTP synthase
#2: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 4 / Formula: C9H16N3O14P3 / Cytidine triphosphate
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: E. coli CTP synthase CC mutant filament / Type: COMPLEX
Details: Disulfide-crosslinked E. coli CTP synthase filaments assembled in non-reducing buffer, bound to CTP and ADP
Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET22b
Buffer solutionpH: 8
SpecimenConc.: 0.15 mg/ml
Details: Filaments were assembled by dialysis in non-reducing buffer (50 mM Na-HEPES, pH 8.0). Products CTP (0.6 mM) and ADP (1.5 mM) were added to filaments.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
4ctffindCTF correction
10SPIDERinitial Euler assignment
11SPIDERfinal Euler assignment
13SPIDER3D reconstruction
14hsearch_lorentz3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 48.2 deg. / Axial rise/subunit: 82.1 Å / Axial symmetry: C1
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 31170 / Symmetry type: HELICAL

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