+Open data
-Basic information
Entry | Database: PDB / ID: 8pnv | ||||||
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Title | Cryo-EM structure of styrene oxide isomerase | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Heme binding protein / Isomerase / Enzyme | ||||||
Function / homology | isomerase activity / membrane / PROTOPORPHYRIN IX CONTAINING FE / Styrene oxide isomerase Function and homology information | ||||||
Biological species | Pseudomonas sp. VLB120 (bacteria) Vicugna pacos (alpaca) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.048 Å | ||||||
Authors | Khanppnavar, B. / Korkhov, B. / Li, X. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of styrene oxide isomerase Authors: Khanppnavar, B. / Korkhov, B. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pnv.cif.gz | 321.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pnv.ent.gz | 262 KB | Display | PDB format |
PDBx/mmJSON format | 8pnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pnv ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pnv | HTTPS FTP |
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-Related structure data
Related structure data | 17786MC 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: 19680.867 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. VLB120 (bacteria) / Strain: Pseudomonas sp. VLB120 / Cell line: Pseudomonas sp. VLB120 / Gene: stdC / Variant: Pseudomonas sp. VLB120 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O50216 #2: Antibody | Mass: 14055.473 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | 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: Styrene oxide isomerase-nanobody complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Pseudomonas sp. VLB120 (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||||||
3D reconstruction | Resolution: 2.048 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137013 / Symmetry type: POINT |