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Yorodumi- PDB-1w3x: Isopenicillin N synthase d-(L-a-aminoadipoyl)-(3R)-methyl-L-cyste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w3x | ||||||
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Title | Isopenicillin N synthase d-(L-a-aminoadipoyl)-(3R)-methyl-L-cysteine D-a-hydroxyisovaleryl ester complex (Oxygen exposed 5 minutes 20 bar) | ||||||
Components | ISOPENICILLIN N SYNTHETASE | ||||||
Keywords | SYNTHASE / ANTIBIOTIC BIOSYNTHESIS / B-LACTAM ANTIBIOTIC / IRON / OXIDOREDUCTASE / 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: 1.46 Å | ||||||
Authors | Daruzzaman, A. / Clifton, I.J. / Rutledge, P.J. | ||||||
Citation | Journal: Chembiochem / Year: 2006 Title: Unexpected Oxidation of a Depsipeptide Substrate Analogue in Crystalline Isopenicillin N Synthase. Authors: Daruzzaman, A. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w3x.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w3x.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 1w3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/1w3x ftp://data.pdbj.org/pub/pdb/validation_reports/w3/1w3x | HTTPS FTP |
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-Related structure data
Related structure data | 1w3vC 1bk0S S: Starting model for refinement C: citing same article (ref.) |
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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 (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Gene: PCB C / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-W2X / |
#4: Water | ChemComp-HOH / |
Compound details | CATALYTIC ACTIVITY: N-[(5S)-5-AMINO-5-CARBOXYPENTANOYL]-L- CYSTEINYL-D-VALINE + O(2) = ...CATALYTIC ACTIVITY: N-[(5S)-5-AMINO-5-CARBOXYPEN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | pH: 8.5 Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL (PH8.5), pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 9, 2001 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→71 Å / Num. obs: 56205 / % possible obs: 96.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.2 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK0 Resolution: 1.46→57.74 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.465 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.064 / 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: 15.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.46→57.74 Å
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Refine LS restraints |
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