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- PDB-8k03: CryoEM structure of the transketolase ANIP from Streptomyces hygr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k03 | ||||||
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Title | CryoEM structure of the transketolase ANIP from Streptomyces hygrospinosus | ||||||
![]() | Putative transketolase | ||||||
![]() | TRANSFERASE / transketolase / apo form | ||||||
Function / homology | 1-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![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å | ||||||
![]() | Jiang, W.X. / Ma, L.X. / Xing, Q. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.6 KB | Display | ![]() |
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PDB format | ![]() | 157 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 36756MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Noncrystallographic symmetry (NCS) | NCS domain:
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
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Components
#1: Protein | Mass: 62158.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A1V0QSW5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Dimer of the transketolase ANIP / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66525 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.07 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 6.58946215642E-13 Å |