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Yorodumi- PDB-1hjf: Alteration of the co-substrate selectivity of deacetoxycephalospo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hjf | ||||||
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Title | Alteration of the co-substrate selectivity of deacetoxycephalosporin C synthase: The role of arginine-258 | ||||||
Components | DEACETOXYCEPHALOSPORIN C SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / ALTERNATIVE 2-OXOACIDS / CEPHEM ANTIBIOTIC BIOSYNTHESIS / CHEMICAL COSUBSTRATE RESCUE / CO-SUBSTRATE SELECTIVITY / 2- OXOGLUTARATE-DEPENDENT OXYGENASE | ||||||
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: 1.6 Å | ||||||
Authors | Lee, H.J. / Lloyd, M.D. / Clifton, I.J. / Harlos, K. / Dubus, A. / Baldwin, J.E. / Frere, J.M. / Schofield, C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Alteration of the 2-Oxoacid Cosubstrate Selectivity in Deacetoxycephalosporin C Synthase: The Role of Arginine-258 Authors: Lee, H.J. / Lloyd, M.D. / Harlos, K. / Clifton, I.J. / Baldwin, J.E. / Schofield, C.J. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Studies on the Active Site of Deacetoxycephalosporin C Synthase Authors: Lloyd, M.D. / Lee, H.J. / Harlos, K. / Zhang, Z.H. / Baldwin, J.E. / Schofield, C.J. / Charnock, J.M. / Garner, C.D. / Hara, T. / Van Scheltinga, A.C.T. / Valegard, K. / Viklund, J.A.C. / ...Authors: Lloyd, M.D. / Lee, H.J. / Harlos, K. / Zhang, Z.H. / Baldwin, J.E. / Schofield, C.J. / Charnock, J.M. / Garner, C.D. / Hara, T. / Van Scheltinga, A.C.T. / Valegard, K. / Viklund, J.A.C. / Hajdu, J. / Andersson, I. / Danielsson, A. / Bhikhabhai, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hjf.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hjf.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/1hjf ftp://data.pdbj.org/pub/pdb/validation_reports/hj/1hjf | HTTPS FTP |
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-Related structure data
Related structure data | 1hjgC 1rxgS 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: 34562.574 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: IRON(II) AND ALPHA-KETO-ISOCAPROATE COMPLEX OF MUTANT ENZYME Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) Description: RECOMBINANT ENZYME OF S. CLAVULIGERUS ENZYME. R258Q MUTANT ENZYME Gene: CEFE, R258Q MUTANT / Plasmid: PET24A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P18548 |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-COI / |
#4: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED MUTATION ARG258GLN DAOCS CATALYZES THE REACTION FROM PENICILLIN N TO DEACETOXY- ...CHAIN A ENGINEERED |
Sequence details | RESIDUE A50 BUILT AS ILE (AS REPORTED IN PATENT) NOT LEU (AS REPORTED IN PAPER) SIDECHAIN OF GLN- ...RESIDUE A50 BUILT AS ILE (AS REPORTED IN PATENT) NOT LEU (AS REPORTED IN PAPER) SIDECHAIN OF GLN-258 DISORDERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.78 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP AT 20 DEGREES C. 100 MM HEPES-NAOH, PH 7.0, 6% (W/V) GLYCEROL, 5 MM 2-OXO-4-METHYLPENTANOATE, 1.5-1.7 M AMMONIUM SULPHATE CRYSTALS SOAKED IN 5 MM IRON(II) SULPHATE IN MOTHER ...Details: HANGING DROP AT 20 DEGREES C. 100 MM HEPES-NAOH, PH 7.0, 6% (W/V) GLYCEROL, 5 MM 2-OXO-4-METHYLPENTANOATE, 1.5-1.7 M AMMONIUM SULPHATE CRYSTALS SOAKED IN 5 MM IRON(II) SULPHATE IN MOTHER LIQUOR UNDER ANAEROBIC CONDITIONS BEFORE DATA COLLECTION. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 14 ℃ / 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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 1999 |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 32966 / % possible obs: 95.7 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 1 / % possible all: 95.7 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 122299 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RXG Resolution: 1.6→19.38 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1783912 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DATA DETWINNED BEFORE REFINEMENT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.9845 Å2 / ksol: 0.396472 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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