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Yorodumi- PDB-1bk0: ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE COMPLEX) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bk0 | ||||||
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Title | ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ACV-FE COMPLEX) | ||||||
Components | ISOPENICILLIN N SYNTHASE | ||||||
Keywords | 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: 1.3 Å | ||||||
Authors | Roach, P.L. / Clifton, I.J. / Hensgens, C.M.H. / Shibata, N. / Schofield, C.J. / Hajdu, J. / Baldwin, J.E. | ||||||
Citation | 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. #1: 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. #2: 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 | 1bk0.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bk0.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bk0_validation.pdf.gz | 689.3 KB | Display | wwPDB validaton report |
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Full document | 1bk0_full_validation.pdf.gz | 690.1 KB | Display | |
Data in XML | 1bk0_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1bk0_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bk0 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bk0 | HTTPS FTP |
-Related structure data
Related structure data | 1blzC 1ipsS 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 (mold) / Gene: PCB C / Plasmid: PJB703 / Production host: Escherichia coli (E. coli) / Strain (production host): NM554 / References: UniProt: P05326 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-ACV / |
#5: 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: 2.32 Å3/Da / Density % sol: 47 % | |||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | |||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / Details: Roach, P.L., (1996) Eur. J. Biochem., 242, 736. | |||||||||||||||
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: ESRF / Beamline: BM14 / Wavelength: 0.997 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→25 Å / Num. obs: 80233 / % possible obs: 95.4 % / Redundancy: 3.21 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.1 / % possible all: 93.2 |
Reflection | *PLUS Num. measured all: 267069 |
Reflection shell | *PLUS % possible obs: 93.2 % / Num. unique obs: 7714 / Num. measured obs: 25182 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IPS Resolution: 1.3→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT AND EXTRA STATISTICS GENERATED WITH X-PLOR 3.851. ESD FROM LUZZATI PLOT (A) : 0.13 LOW RESOLUTION CUTOFF (A) : 5.0
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Displacement parameters | Biso mean: 11.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→12.5 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1725 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |