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- PDB-9uz6: Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo -

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Basic information

Entry
Database: PDB / ID: 9uz6
TitleCryo-EM structure of E. coli glycine decarboxylase (P-protein) apo
ComponentsGlycine dehydrogenase (decarboxylating)
KeywordsOXIDOREDUCTASE / (de)carboxylase / PLP-dependent enzymes / dimer
Function / homology
Function and homology information


glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / glycine binding / one-carbon metabolic process / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
Glycine dehydrogenase (decarboxylating) / Glycine cleavage system P protein / : / : / Glycine cleavage system P-protein / Glycine dehydrogenase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Glycine dehydrogenase (decarboxylating)
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. DH10B (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsHan, Z. / Zeng, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo
Authors: Han, Z. / Zeng, A.
History
DepositionMay 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 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: Glycine dehydrogenase (decarboxylating)
B: Glycine dehydrogenase (decarboxylating)


Theoretical massNumber of molelcules
Total (without water)211,2332
Polymers211,2332
Non-polymers00
Water00
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 Glycine dehydrogenase (decarboxylating) / Glycine cleavage system P-protein / Glycine decarboxylase / Glycine dehydrogenase (aminomethyl-transferring)


Mass: 105616.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. DH10B (bacteria)
Gene: gcvP, b2903, JW2871 / Production host: Cloning vector pET-28a-ZaTdT12 (others)
References: UniProt: P33195, glycine dehydrogenase (aminomethyl-transferring)
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: Dimer complex of glycine (de)carboxylating apo open form
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.104 MDa / Experimental value: YES
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: pET-28a
Buffer solutionpH: 7.4 / Details: pH=7.5
Buffer componentConc.: 20 mg/mL / Name: Tri (Hydroxymethyl) Amino Methane Hydrochloride / Formula: Tris-HCl
SpecimenConc.: 1.28 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 287 K

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Electron microscopy imaging

MicroscopyModel: SHUIMU TOTEM 300S
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 60000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 100 K / Temperature (min): 90 K
Image recordingAverage exposure time: 3.29 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5490
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3153680
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1975829 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 106.5 / Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingChain residue range: 3-952 / Details: ModelSMART / Source name: Other / Type: in silico model
RefinementHighest resolution: 2.32 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314478
ELECTRON MICROSCOPYf_angle_d0.51519676
ELECTRON MICROSCOPYf_dihedral_angle_d4.3261998
ELECTRON MICROSCOPYf_chiral_restr0.0432246
ELECTRON MICROSCOPYf_plane_restr0.0042584

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