+Open data
-Basic information
Entry | Database: PDB / ID: 3zku | ||||||
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Title | Isopenicillin N synthase with substrate analogue AhCV | ||||||
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: 1.4 Å | ||||||
Authors | Daruzzaman, A. / Clifton, I.J. / Rutledge, P.J. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: The Interaction of Isopenicillin N Synthase with Homologated Substrate Analogues Delta-(L-Alpha-Aminoadipoyl)-L-Homocysteinyl-D-Xaa Characterised by Protein Crystallography. 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 | 3zku.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zku.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/3zku ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zku | HTTPS FTP |
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-Related structure data
Related structure data | 3zkyC 1bk0S 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, isopenicillin-N synthase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-HCV / |
#4: 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: 46 % / 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 SUBSTRATE, 25MG/ML IPNS |
-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: MARRESEARCH / Detector: CCD / Date: Apr 27, 2002 / Details: MIRROR |
Radiation | Monochromator: DIAMOND (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42 Å / Num. obs: 66426 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.6 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK0 Resolution: 1.4→41.22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.475 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→41.22 Å
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Refine LS restraints |
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