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Yorodumi- PDB-1qje: Isopenicillin N synthase from Aspergillus nidulans (IP1 - Fe complex) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qje | ||||||
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Title | Isopenicillin N synthase from Aspergillus nidulans (IP1 - Fe complex) | ||||||
Components | ISOPENICILLIN ... | ||||||
Keywords | B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS / ENZYME-PRODUCT COMPLEX | ||||||
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: 1.35 Å | ||||||
Authors | Burzlaff, N.I. / Clifton, I.J. / Rutledge, P.J. / Roach, P.L. / Adlington, R.M. / Baldwin, J.E. | ||||||
Citation | 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.H. / Pickford, M. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E. #1: 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. #2: 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. #3: Journal: Protein Sci. / Year: 1995 Title: Crystallization and Preliminary X-Ray Diffraction Studies on Recombinant Isopenicillin N Synthase from Aspergillus Nidulans Authors: Roach, P.L. / Schofield, C.J. / Baldwin, J.E. / Clifton, I.J. / Hajdu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qje.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qje.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qje ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qje | HTTPS FTP |
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-Related structure data
Related structure data | 1qiqC 1qjfC 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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Details | BIOLOGICAL_UNIT: MONOMER |
-Components
-ISOPENICILLIN ... , 1 types, 1 molecules A
#1: Protein | Mass: 37563.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Gene: PCB C / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326 |
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-Non-polymers , 5 types, 496 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-IP1 / |
#4: Chemical | ChemComp-ACV / |
#5: Chemical | ChemComp-FE2 / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | IN THIS COMPLEX THE MOLECULES OF ISOPENICILLIN N (IP1) AND L-A-(D-AMINOADIPOYL)-L-CYSTEINYL-D- ...IN THIS COMPLEX THE MOLECULES OF ISOPENICIL |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.226 Å3/Da / Density % sol: 37 % | |||||||||||||||
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Crystal grow | pH: 8.5 Details: 1.8M LITHIUM SULPHATE, 100MM TRIS/HCL (PH8.5), (5MM FERROUS SULPHATE, 70 MM ACMC, 50MG/ML IPNS), pH 8.50 | |||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→25 Å / Num. obs: 69285 / % possible obs: 92.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.0078 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.35→1.37 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.8 / % possible all: 43 |
Reflection | *PLUS Num. measured all: 404650 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 43 % / Num. unique obs: 1595 / Num. measured obs: 9310 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BK0 Resolution: 1.35→25 Å / Num. restraintsaints: 34969 / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 2516.4 / Occupancy sum non hydrogen: 3131.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→25 Å
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Refine LS restraints |
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