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Yorodumi- PDB-2ve1: Isopenicillin N synthase with substrate analogue AsMCOV (oxygen e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ve1 | |||||||||
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Title | Isopenicillin N synthase with substrate analogue AsMCOV (oxygen exposed 1min 20bar) | |||||||||
Components | ISOPENICILLIN N SYNTHETASE | |||||||||
Keywords | OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / PENICILLIN BIOSYNTHESIS / IRON / OXYGENASE / VITAMIN C / METAL-BINDING / MONOCYCLIC INTERMEDIATE / B-LACTAM ANTIBIOTIC | |||||||||
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: 2.2 Å | |||||||||
Authors | Ge, W. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. | |||||||||
Citation | Journal: Chembiochem / Year: 2009 Title: Structural Studies on the Reaction of Isopenicillin N Synthase with a Sterically Demanding Depsipeptide Substrate Analogue. Authors: Ge, W. / Clifton, I.J. / Howard-Jones, A.R. / Stok, J.E. / 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 | 2ve1.cif.gz | 150.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ve1.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ve1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2ve1 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2ve1 | HTTPS FTP |
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-Related structure data
Related structure data | 2vcmC 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-FE2 / |
#3: Chemical | ChemComp-W2X / |
#4: Chemical | ChemComp-M11 / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | D-L-A-AMINOADIPOYL-(3S-METHYL)-L-CYSTEINE D-A-HYDROXYL ISOVALERYL ESTER (M11): SAME, EXCEPT FOR ...D-L-A-AMINOADIPO |
Sequence details | RESIDUES 1-2 NOT SEEN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % / 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: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 10, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60.75 Å / Num. obs: 16731 / % possible obs: 98.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.98 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK0 Resolution: 2.2→60.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.885 / SU B: 11.7 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED BY TLSANL FROM REFMAC TLS MODEL
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→60.75 Å
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Refine LS restraints |
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