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Yorodumi- PDB-1jcl: OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jcl | ||||||
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Title | OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION | ||||||
Components | DEOXYRIBOSE-PHOSPHATE ALDOLASE | ||||||
Keywords | LYASE / alpha-beta TIM barrel | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å | ||||||
Authors | Heine, A. / DeSantis, G. / Luz, J.G. / Mitchell, M. / Wong, C.-H. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jcl.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jcl.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/1jcl ftp://data.pdbj.org/pub/pdb/validation_reports/jc/1jcl | HTTPS FTP |
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-Related 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: 27906.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6L0, deoxyribose-phosphate aldolase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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 |