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Yorodumi- PDB-1e5i: DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e5i | ||||||
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Title | DELTA-R306 DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH IRON AND 2-OXOGLUTARATE. | ||||||
Components | DEACETOXYCEPHALOSPORIN C SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / FERROUS OXYGENASE / CEPHALOSPORIN / 2-OXOGLUTARATE / C-TERMINUS ANTIBIOTICS / OXIDATIVE COUPLING CONTROL | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lee, H.J. / Lloyd, M.D. / Harlos, K. / Clifton, I.J. / Baldwin, J.E. / Schofield, C.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Kinetic and Crystallographic Studies on Deacetoxycephalosporin C Synthase (Daocs) 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 (Daocs) 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. / Terrwisscha Van Scheltinga, A.C. / Valegard, K. / Viklund, ...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. / Terrwisscha Van Scheltinga, A.C. / 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 | 1e5i.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e5i.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/1e5i ftp://data.pdbj.org/pub/pdb/validation_reports/e5/1e5i | HTTPS FTP |
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-Related structure data
Related structure data | 1e5hC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34046.004 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Description: RECOMBINANT E.COLI / Gene: CEFE / Plasmid: PET 24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P18548, deacetoxycephalosporin-C synthase |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-AKG / |
#4: Water | ChemComp-HOH / |
Compound details | THE C-TERMINAL RESIDUES THR, SER, LYS, ALA ARE DELETED. FUNCTION: DAOCS CATALYZES THE STEP FROM ...THE C-TERMINAL RESIDUES THR, SER, LYS, ALA ARE DELETED. FUNCTION: DAOCS CATALYZES THE STEP FROM PENICILLIN |
Sequence details | ILE A 50, WRONGLY REPORTED IN DATABASE |
-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 | pH: 7 Details: 100 MM HEPES-NAOH, PH 7.0, 0.5 MM PB(OAC)2(OH2)2, 5 MM 2-OXOGLUTARATE, GLYCEROL 5-10% (W/V), 1.4-1.65 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 26, 1999 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 17034 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.118 / Net I/σ(I): 3.98 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 6.29 / Rsym value: 0.561 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RXF Resolution: 2.1→19.99 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2222669.75 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: DATA DETWINNED USING CCP4 PROGRAMME DETWIN (A. LESLIE)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.8284 Å2 / ksol: 0.38674 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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