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Yorodumi- PDB-1unb: Deacetoxycephalosporin C synthase complexed with 2-oxoglutarate a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1unb | ||||||
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Title | Deacetoxycephalosporin C synthase complexed with 2-oxoglutarate and ampicillin | ||||||
Components | DEACETOXYCEPHALOSPORIN C SYNTHETASE | ||||||
Keywords | OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS | ||||||
Function / homology | Function and homology information deacetoxycephalosporin-C synthase / deacetoxycephalosporin-C synthase activity / L-ascorbic acid binding / antibiotic biosynthetic process / iron ion binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Valegard, K. / Terwisscha van Scheltinga, A.C. / Dubus, A. / Oster, L.M. / Rhangino, G. / Hajdu, J. / Andersson, I. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: The Structural Basis of Cephalosporin Formation in a Mononuclear Ferrous Enzyme Authors: Valegard, K. / Terwisscha van Scheltinga, A.C. / Dubus, A. / Ranghino, G. / Oster, L.M. / Hajdu, J. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1unb.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1unb.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 1unb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/1unb ftp://data.pdbj.org/pub/pdb/validation_reports/un/1unb | HTTPS FTP |
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-Related structure data
Related structure data | 1uo9C 1uobC 1uofC 1uogC 1rxfS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34591.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P18548, deacetoxycephalosporin-C synthase |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-PN1 / ( |
#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: 2.26 Å3/Da / Density % sol: 45.7 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPESPH7.5, pH 7.50 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Valegard, K., (1998) Nature, 394, 805. / PH range low: 7.5 / PH range high: 7 | ||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 1.076 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.076 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.4 Å / Num. obs: 45847 / % possible obs: 94 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.295 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 45862 / % possible obs: 94.2 % / Num. measured all: 299664 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.312 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RXF Resolution: 1.5→31.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.76 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE RESIDUES MISSING IN THE PDB ENTRY (81-90,167-177 AND 310-311) ARE DISORDERED, AND THEREFORE OMITTED FROM THE MODEL
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→31.5 Å
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Refine LS restraints |
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