[English] 日本語
![](img/lk-miru.gif)
- PDB-8p48: IPNS variant N252D in complex with Fe and ACV under anaerobic con... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8p48 | ||||||
---|---|---|---|---|---|---|---|
Title | IPNS variant N252D in complex with Fe and ACV under anaerobic conditions | ||||||
![]() | Isopenicillin N synthase | ||||||
![]() | OXIDOREDUCTASE / Isopenicillin N synthase / penicillins / biosynthesis / 2OG oxygenases / antibiotic | ||||||
Function / homology | ![]() isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rabe, P. / Schofield, C.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: IPNS variant N252D in complex with Fe and ACV under anaerobic conditions Authors: Rabe, P. / Schofield, C.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 201.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 159.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37564.820 Da / Num. of mol.: 1 / Mutation: N252D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ACV / | #4: Chemical | ChemComp-FE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % / Description: needle morphology, 4 um x 4 um x 160 um |
---|---|
Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1 M Tris pH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryogenic / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 9, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50.58 Å / Num. obs: 39910 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.061 / Rrim(I) all: 0.226 / Χ2: 0.99 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.63→1.67 Å / Redundancy: 13.3 % / Rmerge(I) obs: 3.233 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2869 / CC1/2: 0.545 / Rpim(I) all: 0.902 / Rrim(I) all: 3.359 / Χ2: 0.9 / % possible all: 99.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→50.58 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|