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- PDB-1q0z: Crystal structure of aclacinomycin methylesterase (RdmC) with bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q0z | ||||||
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Title | Crystal structure of aclacinomycin methylesterase (RdmC) with bound product analogue, 10-decarboxymethylaclacinomycin A (DcmA) | ||||||
![]() | aclacinomycin methylesterase | ||||||
![]() | HYDROLASE / Anthracycline / methylesterase / polyketide / Streptomyces / tailoring enzyme / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | ![]() aclacinomycin methylesterase / aclacinomycin T methylesterase activity / : / : / glycerolipid catabolic process / triacylglycerol lipase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jansson, A. / Niemi, J. / Mantsala, P. / Schneider, G. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: Crystal structure of aclacinomycin methylesterase with bound product analogues: implications for anthracycline recognition and mechanism. Authors: Jansson, A. / Niemi, J. / Mantsala, P. / Schneider, G. #1: ![]() Title: Crystallization and preliminary X-ray diffraction studies of aclacinomycin-10-methyl esterase 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.1 KB | Display | ![]() |
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PDB format | ![]() | 56.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.6 KB | Display | ![]() |
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Full document | ![]() | 805.6 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q0rSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31828.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-AKA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-1PE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: Ammonium sulphate, PEG400, Hepes buffer, pH 7.5, VAPOR DIFFUSION, 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→26.31 Å / Num. all: 19636 / Num. obs: 19636 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.106 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.95→2.06 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.413 / % possible all: 99.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 95945 / Rmerge(I) obs: 0.106 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.413 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code 1Q0R, another RdmC+substrate complex Resolution: 1.95→26.31 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
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Displacement parameters | Biso mean: 18 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→26.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.05 Å /
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Refinement | *PLUS % reflection Rfree: 8 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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