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Yorodumi- PDB-2cbo: Crystal structure of the neocarzinostatin 3Tes24 mutant bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cbo | ||||||
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Title | Crystal structure of the neocarzinostatin 3Tes24 mutant bound to testosterone hemisuccinate. | ||||||
Components | NEOCARZINOSTATIN | ||||||
Keywords | ANTIBIOTIC / PHAGE-DISPLAY / HAPTEN BINDING / NEOCARZINOSTATIN / ANTIMICROBIAL / DNA-BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES CARZINOSTATICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Drevelle, A. / Graille, M. / Heyd, B. / Sorel, I. / Ulryck, N. / Pecorari, F. / Desmadril, M. / van Tilbeurgh, H. / Minard, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structures of in Vitro Evolved Binding Sites on Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways. Authors: Drevelle, A. / Graille, M. / Heyd, B. / Sorel, I. / Ulryck, N. / Pecorari, F. / Desmadril, M. / Van Tilbeurgh, H. / Minard, P. #1: Journal: Biochemistry / Year: 2003 Title: In Vitro Evolution of the Binding Specificity of Neocarzinostatin, an Enediyne-Binding Chromoprotein. Authors: Heyd, B. / Pecorari, F. / Collinet, B. / Adjadj, E. / Desmadril, M. / Minard, P. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cbo.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cbo.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/2cbo ftp://data.pdbj.org/pub/pdb/validation_reports/cb/2cbo | HTTPS FTP |
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-Related structure data
Related structure data | 2cbmC 2cbqC 2cbtC 1ncoS 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: 11615.560 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CARZINOSTATICUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR(DE3)PLYSS / References: UniProt: P0A3R9 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | HAS ANTIBIOTIC ACTIVITY FOR GRAM-POSITIVE BACTERIA AND ANTITUMOR ACTIVITY FOR CERTAIN MOUSE TUMORS ...HAS ANTIBIOTIC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 50 % |
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Crystal grow | Details: 1.6-1.7M (NH4)2SO4, 0.1 M SODIUM CITRATE PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 10933 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 1.97 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.6 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NCO Resolution: 1.7→18.51 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 187070.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2945 Å2 / ksol: 0.388351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→18.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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