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- PDB-8zpr: EcGK filament complexed with proline. -

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Basic information

Entry
Database: PDB / ID: 8zpr
TitleEcGK filament complexed with proline.
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 / 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 superfamily ...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 superfamily / PUA domain profile. / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / PUA-like superfamily
Similarity search - Domain/homology
PROLINE / Glutamate 5-kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 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 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,74916
Polymers312,8288
Non-polymers9218
Water10,773598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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
#2: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: EcGK incubated with proline / Type: COMPLEX / Entity ID: #1 / 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
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 481216 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 127.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002621752
ELECTRON MICROSCOPYf_angle_d0.428229464
ELECTRON MICROSCOPYf_chiral_restr0.03973472
ELECTRON MICROSCOPYf_plane_restr0.00343872
ELECTRON MICROSCOPYf_dihedral_angle_d3.81433112

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