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Yorodumi- PDB-2jb4: Isopenicillin N synthase with a 2-thiabicycloheptan-6-one product... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jb4 | ||||||
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Title | Isopenicillin N synthase with a 2-thiabicycloheptan-6-one product analogue | ||||||
Components | Isopenicillin N synthase | ||||||
Keywords | OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / PENICILLIN BIOSYNTHESIS / IRON / OXYGENASE / VITAMIN C / METAL-BINDING / 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 | Stewart, A.C. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. | ||||||
Citation | Journal: Chembiochem / Year: 2007 Title: A Cyclobutanone Analogue Mimics Penicillin in Binding to Isopenicillin N Synthase. Authors: Stewart, A.C. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. #1: Journal: Nature / Year: 1999 Title: The Reaction Cycle of Isopenicillinn 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jb4.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jb4.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 2jb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jb4_validation.pdf.gz | 767.6 KB | Display | wwPDB validaton report |
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Full document | 2jb4_full_validation.pdf.gz | 769.2 KB | Display | |
Data in XML | 2jb4_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 2jb4_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jb4 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jb4 | HTTPS FTP |
-Related structure data
Related structure data | 1bk0S 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
-Protein , 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 (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Gene: ipnA, ips, AN2622 / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase |
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-Non-polymers , 5 types, 408 molecules
#2: Chemical | ChemComp-A14 / ( | ||||
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#3: Chemical | ChemComp-FE / | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.23 Å3/Da / Density % sol: 44.4 % / 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, 6.8 MM 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: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 7, 2003 / Details: RH COATED TOROIDAL MIRRORS |
Radiation | Monochromator: GE (2 2 0) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30.9 Å / Num. obs: 80123 / % possible obs: 96.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 78.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK0 Resolution: 1.3→57.74 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.366 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048 / 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: 7.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→57.74 Å
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Refine LS restraints |
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