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Yorodumi- PDB-8alj: IPNS H270E variant in complex with Fe and ACV after 3 hours O2 ex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8alj | ||||||
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Title | IPNS H270E variant in complex with Fe and ACV after 3 hours 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: 1.68 Å | ||||||
Authors | Rabe, P. / Schfoeidl, C.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: IPNS H270E variant in complex with Fe and ACV after 3 hours O2 exposure Authors: Rabe, P. / Schfoeidl, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8alj.cif.gz | 201.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8alj.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 8alj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8alj_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8alj_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8alj_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 8alj_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/8alj ftp://data.pdbj.org/pub/pdb/validation_reports/al/8alj | HTTPS FTP |
-Related structure data
Related structure data | 6zaeS S: Starting model for refinement |
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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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Unit cell |
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-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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05326, isopenicillin-N synthase | ||||||||
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#2: Chemical | #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 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.39 % / Description: needle morphology, 4 um x 4 um x 150 um |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 8.3 / Details: 1.7 M Li2SO4, 0.1 M Tris pH8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2022 | |||||||||||||||||||||
Radiation | Monochromator: 0.9763 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.68→59.98 Å / Num. obs: 36274 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.075 / Rrim(I) all: 0.277 / Net I/σ(I): 7.6 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZAE Resolution: 1.68→59.98 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.55 Å2 / Biso mean: 25.6129 Å2 / Biso min: 11.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→59.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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