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Yorodumi- PDB-1odn: ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN-EXPOSE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1odn | ||||||
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Title | ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN-EXPOSED PRODUCT FROM ANAEROBIC AC-VINYLGLYCINE FE COMPLEX) | ||||||
Components | ISOPENICILLIN N SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS | ||||||
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 | EMERICELLA NIDULANS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Elkins, J.M. / Rutledge, P.J. / Burzlaff, N.I. / Clifton, I.J. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2003 Title: Crystallographic Studies on the Reaction of Isopenicillin N Synthase with an Unsaturated Substrate Analogue Authors: Elkins, J.M. / Rutledge, P.J. / Burzlaff, N.I. / Clifton, I.J. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E. #1: Journal: Nature / Year: 1999 Title: The Reaction Cycle of Isopenicillin N Synthase Observed by X-Ray Diffraction Authors: Burzlaff, N.I. / Rutledge, P.J. / Clifton, I.J. / Hensgens, C.M.H. / Pickford, M. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E. #2: Journal: Nature / Year: 1997 Title: Structure of Isopenicillin N Synthase Complexed with Substrate and the Mechanism of Penicillin Formation Authors: Roach, P.L. / Clifton, I.J. / Hensgens, C.M. / Shibata, N. / Schofield, C.J. / Hajdu, J. / Baldwin, J.E. #3: Journal: Nature / Year: 1995 Title: Crystal Structure of Isopenicillin N Synthase is the First from a New Structural Family of Enzymes Authors: Roach, P.L. / Clifton, I.J. / Fulop, V. / Harlos, K. / Barton, G.J. / Hajdu, J. / Andersson, I. / Schofield, C.J. / Baldwin, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1odn.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1odn.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 1odn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/1odn ftp://data.pdbj.org/pub/pdb/validation_reports/od/1odn | HTTPS FTP |
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-Related structure data
Related structure data | 1odmC 1qjeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37563.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326 |
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#2: Chemical | ChemComp-APV / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-FE2 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 40 % | |||||||||||||||
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Crystal grow | pH: 7.5 Details: 1.8M LITHIUM SULPHATE, 100MM TRIS/HCL (PH8.5), (5MM FERROUS SULPHATE, 70 MM ACVG, 50MG/ML IPNS), pH 7.50 | |||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop / Details: Roach, P.L., (1996) Eur. J. Biochem., 242, 736. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 0.9312 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9312 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→41.17 Å / Num. obs: 42669 / % possible obs: 95.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 41.17 Å / Redundancy: 2.4 % / Num. measured all: 101990 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 94.2 % / Redundancy: 2.4 % / Num. unique obs: 6077 / Num. measured obs: 14387 / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJE Resolution: 1.6→38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.359 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→38 Å
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Refine LS restraints |
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