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- PDB-1jcl: OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jcl | ||||||
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Title | OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION | ||||||
![]() | DEOXYRIBOSE-PHOSPHATE ALDOLASE | ||||||
![]() | LYASE / alpha-beta TIM barrel | ||||||
Function / homology | ![]() deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / nucleobase-containing small molecule interconversion / carbohydrate catabolic process / lyase activity / DNA damage response / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heine, A. / DeSantis, G. / Luz, J.G. / Mitchell, M. / Wong, C.-H. / Wilson, I.A. | ||||||
![]() | ![]() Title: Observation of covalent intermediates in an enzyme mechanism at atomic resolution. Authors: Heine, A. / DeSantis, G. / Luz, J.G. / Mitchell, M. / Wong, C.H. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.2 KB | Display | ![]() |
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PDB format | ![]() | 182.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
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Full document | ![]() | 439.1 KB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 27906.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.98 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: MPEG 5000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→30 Å / Num. all: 256887 / Num. obs: 256887 / % possible obs: 95.5 % / Redundancy: 2.5 % / Rsym value: 0.063 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.05→1.07 Å / Mean I/σ(I) obs: 1 / Rsym value: 0.667 / % possible all: 64 |
Reflection | *PLUS Num. measured all: 638223 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 64 % / Rmerge(I) obs: 0.667 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: native DERA Resolution: 1.05→10 Å / Num. parameters: 40900 / Num. restraintsaints: 48367 / Cross valid method: R-free / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 7 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→10 Å /
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor all: 0.143 / Rfactor Rwork: 0.143 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |