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- PDB-2wo7: Isopenicillin N synthase with substrate analogue L,L,D-ACd2Ab (un... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wo7 | ||||||
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Title | Isopenicillin N synthase with substrate analogue L,L,D-ACd2Ab (unexposed) | ||||||
![]() | ISOPENICILLIN N SYNTHASE | ||||||
![]() | OXIDOREDUCTASE / B-LACTAM ANTIBIOTIC / METAL-BINDING / MONOCYCLIC INTERMEDIATE / OXYGENASE / PENICILLIN BIOSYNTHESIS | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ge, W. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. | ||||||
![]() | ![]() Title: Crystallographic Studies on the Binding of Selectively Deuterated Lld- and Lll-Substrate Epimers by Isopenicillin N Synthase. Authors: Ge, W. / Clifton, I.J. / Stok, J.E. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.3 KB | Display | ![]() |
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PDB format | ![]() | 65.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 685.9 KB | Display | ![]() |
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Full document | ![]() | 690.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vbpC ![]() 1bk0S 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-FE2 / |
#3: Chemical | ChemComp-ASV / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | D-L-A-AMINOADIPOYL-L-CYSTEINYL-D-2-AMINO-3, 3DIDEUTERIOBUTYRATE (ASV): DI-DEUTERATED ON BETA CARBON ...D-L-A-AMINOADIPO |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.41 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL, PH 8.5, 2.0MM FERROUS SULPHATE, 2.6MG/ML TRIPEPTIDE, 25MG/ML IPNS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 23, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41.5 Å / Num. obs: 11384 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BK0 Resolution: 2.5→60.75 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.814 / SU B: 24.97 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U VALUES FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.091 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→60.75 Å
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Refine LS restraints |
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