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- PDB-8k03: CryoEM structure of the transketolase ANIP from Streptomyces hygr... -

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Basic information

Entry
Database: PDB / ID: 8k03
TitleCryoEM structure of the transketolase ANIP from Streptomyces hygrospinosus
ComponentsPutative transketolase
KeywordsTRANSFERASE / transketolase / apo form
Function / homology1-deoxy-D-xylulose-5-phosphate synthase activity / Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / terpenoid biosynthetic process / Thiamin diphosphate-binding fold / magnesium ion binding / Putative transketolase
Function and homology information
Biological speciesStreptomyces hygrospinosus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsJiang, W.X. / Ma, L.X. / Xing, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the transketolase ANIP from Streptomyces hygrospinosus
Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q.
History
DepositionJul 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 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: Putative transketolase
B: Putative transketolase


Theoretical massNumber of molelcules
Total (without water)124,3172
Polymers124,3172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 581 / Label seq-ID: 1 - 581

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA

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Components

#1: Protein Putative transketolase / ANIP


Mass: 62158.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygrospinosus (bacteria) / Gene: aniP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1V0QSW5

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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 of the transketolase ANIP / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Salmonella (bacteria)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66525 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 100.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00348920
ELECTRON MICROSCOPYf_angle_d0.625612162
ELECTRON MICROSCOPYf_chiral_restr0.04371406
ELECTRON MICROSCOPYf_plane_restr0.0041608
ELECTRON MICROSCOPYf_dihedral_angle_d4.8941278
Refine LS restraints NCSType: NCS constraints / Rms dev position: 6.58946215642E-13 Å

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