+Open data
-Basic information
Entry | Database: PDB / ID: 8k3h | |||||||||
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Title | Cryo-EM structure of PseP with NAD at 2.86 angstrom resolution | |||||||||
Components | PseP | |||||||||
Keywords | LYASE / altemicidin / pyridoxal 5'-phosphate / PLP-dependent enzyme | |||||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE Function and homology information | |||||||||
Biological species | Pseudomonas fluorescens (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Mori, T. / Awakawa, T. / Adachi, N. / Abe, I. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of PseP with NAD at 2.86 angstrom resolution Authors: Mori, T. / Awakawa, T. / Adachi, N. / Abe, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k3h.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k3h.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 8k3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k3h_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8k3h_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8k3h_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 8k3h_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/8k3h ftp://data.pdbj.org/pub/pdb/validation_reports/k3/8k3h | HTTPS FTP |
-Related structure data
Related structure data | 36851MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 90951.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Production host: Streptomyces lividans TK24 (bacteria) #2: Chemical | Has ligand of interest | Y | |
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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 |
-Sample preparation
Component | Name: PseP / Type: COMPLEX Details: PLP-dependent enzyme in the biosynthesis of altemicidin Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.09 MDa / Experimental value: YES |
Source (natural) | Organism: Pseudomonas fluorescens (bacteria) |
Source (recombinant) | Organism: Streptomyces lividans TK24 (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono-disperse. |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3006 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2478450 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 462772 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
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