+Open data
-Basic information
Entry | Database: PDB / ID: 1rxf | ||||||
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Title | DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II) | ||||||
Components | DEACETOXYCEPHALOSPORIN C SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / FERROUS OXYGENASE / CEPHALOSPORIN / 2-OXOGLUTARATE / ANTIBIOTICS / MEROHEDRAL TWINNING | ||||||
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 / MIR / Resolution: 1.5 Å | ||||||
Authors | Valegard, K. / Terwisscha Van Scheltinga, A.C. / Lloyd, M.D. / Hara, T. / Ramaswamy, S. / Perrakis, A. / Thompson, A. / Lee, H.J. / Baldwin, J.E. / Schofield, C.J. ...Valegard, K. / Terwisscha Van Scheltinga, A.C. / Lloyd, M.D. / Hara, T. / Ramaswamy, S. / Perrakis, A. / Thompson, A. / Lee, H.J. / Baldwin, J.E. / Schofield, C.J. / Hajdu, J. / Andersson, I. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Structure of a cephalosporin synthase. Authors: Valegard, K. / van Scheltinga, A.C. / Lloyd, M.D. / Hara, T. / Ramaswamy, S. / Perrakis, A. / Thompson, A. / Lee, H.J. / Baldwin, J.E. / Schofield, C.J. / Hajdu, J. / Andersson, I. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 1994 Title: Substrate Specificity of Recombinant Streptomyces Clavuligerus Deacetoxycephalosporin C Synthase Authors: Morgan, N. / Pereira, I.A.C. / Andersson, I. / Adlington, R.M. / Baldwin, J.E. / Cole, S.E. / Crouch, N.P. / Sutherland, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rxf.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxf.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxf ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxf | HTTPS FTP |
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-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: 34591.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: PET 11A / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P18548 |
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#2: Chemical | ChemComp-FE / |
#3: 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: 2.6 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / PH range low: 7.5 / PH range high: 7 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39 Å / Num. obs: 45516 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.296 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 193504 |
Reflection shell | *PLUS % possible obs: 95 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→20 Å / Num. parameters: 19389 / Num. restraintsaints: 24240 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: REFINED AGAINST MEROHEDRALLY TWINNED INTENSITIES
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 1974 / Occupancy sum non hydrogen: 2241 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.047 |