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Yorodumi- PDB-1r00: Crystal structure of aclacinomycin-10-hydroxylase (RdmB) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r00 | ||||||
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Title | Crystal structure of aclacinomycin-10-hydroxylase (RdmB) in complex with S-adenosyl-L-homocysteine (SAH) | ||||||
Components | aclacinomycin-10-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / TRANSFERASE / Anthracycline / hydroxylase / methyltransferase / polyketide / Streptomyces / tailoring enzyme | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / O-methyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces purpurascens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / fft / Resolution: 2.5 Å | ||||||
Authors | Jansson, A. / Niemi, J. / Lindqvist, Y. / Mantsala, P. / Schneider, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of Aclacinomycin-10-Hydroxylase, a S-Adenosyl-L-Methionine-dependent Methyltransferase Homolog Involved in Anthracycline Biosynthesis in Streptomyces purpurascens. Authors: Jansson, A. / Niemi, J. / Lindqvist, Y. / Mantsala, P. / Schneider, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and preliminary X-ray diffraction studies of aclacinomycin-10-methylesterase and aclacinomycin-10-hydroxylase from Streptomyces purpurascens Authors: Jansson, A. / Niemi, J. / Mantsala, P. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r00.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r00.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1r00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/1r00 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/1r00 | HTTPS FTP |
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-Related structure data
Related structure data | 1qzzSC 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: 39837.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces purpurascens (bacteria) / Gene: rdmb / Plasmid: pRDM16 / Production host: Escherichia coli (E. coli) / Strain (production host): XL2-blue / References: UniProt: Q54527 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-SAH / |
#4: 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: 2.1 Å3/Da / Density % sol: 41.52 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG4000, ammonium acetate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: MAX II / Beamline: I711 / Wavelength: 1.076 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 9, 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: 2.5→30 Å / Num. all: 12651 / Num. obs: 12651 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.108 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 5.6 / Rsym value: 0.252 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 96318 / Rmerge(I) obs: 0.108 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.252 |
-Processing
Software |
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Refinement | Method to determine structure: fft Starting model: PDB entry 1QZZ, SAM-complex Resolution: 2.5→30 Å Isotropic thermal model: Individual isotropic B-factors for each atom Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood Details: riding hydrogens; the occupancy is put to zero on the sidechains of Gln15, Asp57, Lys84, Glu219, Arg298, Arg319
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å /
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Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 9 % / Rfactor Rfree: 0.28 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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