[English] 日本語
Yorodumi- PDB-8ali: IPNS H270E variant in complex with Fe and ACV after 30 min O2 exposure -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ali | ||||||
---|---|---|---|---|---|---|---|
Title | IPNS H270E variant in complex with Fe and ACV after 30 min O2 exposure | ||||||
Components | Isopenicillin N synthase | ||||||
Keywords | OXIDOREDUCTASE / Isopenicillin N synthase / antibiotic production / O2 binding / reactive intermediate | ||||||
Function / homology | Function and homology information isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | Aspergillus nidulans FGSC A4 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Rabe, P. / Schfoeidl, C.J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: IPNS H270E variant in complex with Fe and ACV after 30 min O2 exposure Authors: Rabe, P. / Schfoeidl, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ali.cif.gz | 201.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ali.ent.gz | 160.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ali.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/8ali ftp://data.pdbj.org/pub/pdb/validation_reports/al/8ali | HTTPS FTP |
---|
-Related structure data
Related structure data | 6zaeS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37554.805 Da / Num. of mol.: 1 / Mutation: H270E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ipnA, ips, AN2622 / Plasmid: pCold_IPNS / Details (production host): pCold_IPNS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACV / | #4: Chemical | ChemComp-FE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.05 % / Description: needle morphology, 4 um x 4 um x 180 um |
---|---|
Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2So4, O.1 M Tris pH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 15, 2022 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.6→59.86 Å / Num. obs: 41690 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 18.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.047 / Rrim(I) all: 0.174 / Net I/σ(I): 9.5 / Num. measured all: 554545 / Scaling rejects: 4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZAE Resolution: 1.6→59.86 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.1 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.81 Å2 / Biso mean: 26.2178 Å2 / Biso min: 12.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→59.86 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|