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- PDB-1odm: ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC AC-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1odm | ||||||
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Title | ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBIC AC-VINYLGLYCINE FE COMPLEX) | ||||||
![]() | ISOPENICILLIN N SYNTHASE | ||||||
![]() | OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS / IRON | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Elkins, J.M. / Rutledge, P.J. / Burzlaff, N.I. / Clifton, I.J. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.7 KB | Display | ![]() |
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PDB format | ![]() | 131.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 708.9 KB | Display | ![]() |
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Full document | ![]() | 710.3 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1odnC ![]() 1qjeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Plasmid: PJB703 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-ASV / | ||||
#3: Chemical | #4: Chemical | ChemComp-FE2 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 ℃ / 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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 17, 1999 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9312 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→29.11 Å / Num. obs: 115554 / % possible obs: 96.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 5.3 / % possible all: 78.9 |
Reflection | *PLUS Highest resolution: 1.15 Å / Lowest resolution: 29.11 Å / Redundancy: 3.3 % / Num. measured all: 375623 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 78.9 % / Redundancy: 1.7 % / Num. unique obs: 13622 / Num. measured obs: 23648 / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 5.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QJE Resolution: 1.15→55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.373 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.031 / 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: 8.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→55 Å
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Refine LS restraints |
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