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- PDB-5u05: Cryo-EM structure of the E. coli CTP synthase tetramer -

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Basic information

Entry
Database: PDB / ID: 5u05
TitleCryo-EM structure of the E. coli CTP synthase tetramer
DescriptorCTP synthase (E.C.6.3.4.2)
KeywordsLIGASE / nucleotide metabolism / enzyme / active
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (7.9 Å resolution / Particle / Single particle)
AuthorsLynch, E.M. / Hicks, D.R. / Kollman, J.M.
CitationNat. Struct. Mol. Biol., 2017, 24, 507-514

Nat. Struct. Mol. Biol., 2017, 24, 507-514 StrPapers
Human CTP synthase filament structure reveals the active enzyme conformation.
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: Nov 22, 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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Assembly

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


Theoretical massNumber of molelcules
Total (without water)241,7884
Polyers241,7884
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)6260
ΔGint (kcal/M)-39
Surface area (Å2)85480

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Components

#1: Polypeptide(L)
CTP synthase / Cytidine 5'-triphosphate synthase / Cytidine triphosphate synthetase / CTPS / UTP--ammonia ligase


Mass: 60446.980 Da / Num. of mol.: 4
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: B7MLA1, EC: 6.3.4.2

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: E. coli CTP synthase tetramer / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli
Source (recombinant)Organism: Escherichia coli / Plasmid: pET22
Buffer solutionpH: 8
SpecimenConc.: 0.3 mg/ml
Details: 50 mM HEPES potassium, pH 8.0, 10 mM magnesium chloride, 0.6 mM UTP, 1.5 mM AMP-PNP, 0.2 mM GTP, 10 mM glutamine
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 FIELD
Image recordingElectron dose: 68 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategoryImage processing ID
1DoG PickerPARTICLE SELECTION1
4cctfindCTF CORRECTION1
5RELIONCTF CORRECTION1
11RELIONINITIAL EULER ASSIGNMENT1
12RELIONFINAL EULER ASSIGNMENT1
14RELIONRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: D2
3D reconstructionResolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6407 / Symmetry type: POINT

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