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Yorodumi- PDB-2ivi: Isopenicillin N Synthase From Aspergillus Nidulans (Anaerobic Ac-... -
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-Basic information
Entry | Database: PDB / ID: 2ivi | ||||||
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Title | Isopenicillin N Synthase From Aspergillus Nidulans (Anaerobic Ac- methyl-cyclopropylglycine Fe Complex) | ||||||
Components | ISOPENICILLIN N SYNTHETASE | ||||||
Keywords | OXIDOREDUCTASE / ANTBIOTIC BIOSYNTHESIS / ANTIBIOTIC BIOSYNTHESIS / IRON / OXYGENASE / VITAMIN C / METAL-BINDING / PENICILLIN BIOSYNTHESIS / 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: 1.3 Å | ||||||
Authors | Elkins, J.M. / Howard-Jones, A.R. / Clifton, I.J. / Roach, P.L. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Interactions of Isopenicillin N Synthase with Cyclopropyl-Containing Substrate Analogues Reveal New Mechanistic Insight. Authors: Howard-Jones, A.R. / Elkins, J.M. / Clifton, I.J. / Roach, P.L. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. #1: Journal: Nature / Year: 1999 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. / Pickford, M. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E. #2: Journal: Nature / Year: 1997 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: Journal: Nature / Year: 1995 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ivi.cif.gz | 162.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ivi.ent.gz | 127.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ivi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ivi_validation.pdf.gz | 695.8 KB | Display | wwPDB validaton report |
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Full document | 2ivi_full_validation.pdf.gz | 696.2 KB | Display | |
Data in XML | 2ivi_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 2ivi_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2ivi ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2ivi | HTTPS FTP |
-Related 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) 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-ACW / | ||||||
#3: Chemical | #4: Chemical | ChemComp-FE2 / | #5: Water | ChemComp-HOH / | Compound details | REMOVES, IN THE PRESENCE OF OXYGEN, 4 HYDROGEN ATOMS FROM DELTA-L-(ALPHA-AMINOADIPYL)-L-CYSTEINYL-D- ...REMOVES, IN THE PRESENCE OF OXYGEN, 4 HYDROGEN ATOMS FROM DELTA-L-(ALPHA-AMINOADIPY | |
-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: 40 % |
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Crystal grow | pH: 8.5 Details: 1.8M LITHIUM SULPHATE, 100MM TRIS/HCL (PH8.5), (5MM FERROUS SULPHATE, 70 MM ACCPG, 50MG/ML IPNS), pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.935 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 3, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→46.57 Å / Num. obs: 353040 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 95.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→58.03 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.25 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→58.03 Å
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