[English] 日本語
Yorodumi- PDB-8jzl: CryoEM structure of the Salmonella effector inositol phosphate ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jzl | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB | ||||||
Components | Inositol phosphate phosphatase SopB | ||||||
Keywords | LIPID BINDING PROTEIN / Type III secretion system / inositol phosphate phosphatase / bacteria effector | ||||||
Function / homology | Function and homology information negative regulation of signaling / symbiont-containing vacuole / lipid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of protein kinase activity / positive regulation of DNA replication / molecular function activator activity / cell periphery / negative regulation of cell growth Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å | ||||||
Authors | Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: CryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jzl.cif.gz | 506.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jzl.ent.gz | 412.9 KB | Display | PDB format |
PDBx/mmJSON format | 8jzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jzl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jzl_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8jzl_validation.xml.gz | 91.1 KB | Display | |
Data in CIF | 8jzl_validation.cif.gz | 138.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/8jzl ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jzl | HTTPS FTP |
-Related structure data
Related structure data | 36746MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 64 - 561 / Label seq-ID: 1 - 498
NCS oper:
|
-Components
#1: Protein | Mass: 55052.680 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Gene: sopB, sigD, STM1091 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O30916, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Homohexamer of inositol phosphate phosphatase SopB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.2 |
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241912 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 134.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
|