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- PDB-8zpj: EcGK bundle at APO state. -

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Basic information

Entry
Database: PDB / ID: 8zpj
TitleEcGK bundle at APO state.
ComponentsGlutamate 5-kinase
KeywordsTRANSFERASE / Proline biosynthesis / amino acid kinase
Function / homology
Function and homology information


proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding ...proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / Glutamate/acetylglutamate kinase / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. ...Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / Glutamate/acetylglutamate kinase / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / PUA-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsZhang, T. / Leng, Q. / Liu, L.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: EcGPR tetramer with catalytic intermediates
Authors: Zhang, T. / Leng, Q. / Liu, L.J.
History
DepositionMay 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase


Theoretical massNumber of molelcules
Total (without water)312,8288
Polymers312,8288
Non-polymers00
Water00
1
A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase

A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
E: Glutamate 5-kinase
F: Glutamate 5-kinase
G: Glutamate 5-kinase
H: Glutamate 5-kinase


Theoretical massNumber of molelcules
Total (without water)3,753,93296
Polymers3,753,93296
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation11
identity operation1_555x,y,z1

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Components

#1: Protein
Glutamate 5-kinase / Gamma-glutamyl kinase / GK


Mass: 39103.457 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: proB, b0242, JW0232 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P0A7B5, glutamate 5-kinase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: EcGK at APO state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
13cryoSPARC4.4.13D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 85.85 ° / Axial rise/subunit: 21 Å / Axial symmetry: C1
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 512330 / Symmetry type: HELICAL
RefinementCross valid method: NONE

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