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Yorodumi- PDB-1n7k: Unique tetrameric structure of deoxyribose phosphate aldolase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n7k | ||||||
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Title | Unique tetrameric structure of deoxyribose phosphate aldolase from Aeropyrum pernix | ||||||
Components | deoxyribose-phosphate aldolase | ||||||
Keywords | LYASE / ALDOLASE / A.pernix / TETRAMER / ALPHA-BETA TIM BARREL / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / protein tetramerization / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å | ||||||
Authors | Tsuge, H. / Sakuraba, H. / Shimoya, I. / Katunuma, N. / Ago, H. / Miyano, M. / Ohshima, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The First Crystal Structure of Archaeal Aldolase. UNIQUE TETRAMERIC STRUCTURE of 2-DEOXY-D-RIBOSE-5-PHOSPHATE ALDOLASE FROM THE HYPERTHERMOPHILIC ARCHAEA Aeropyrum pernix. Authors: Sakuraba, H. / Tsuge, H. / Shimoya, I. / Kawakami, R. / Goda, S. / Kawarabayasi, Y. / Katunuma, N. / Ago, H. / Miyano, M. / Ohshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n7k.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n7k.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n7k ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n7k | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological tetramer is generated by the crystallographic two fold axis |
-Components
#1: Protein | Mass: 24425.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y948, deoxyribose-phosphate aldolase #2: 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: 2.83 Å3/Da / Density % sol: 56.52 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2002 |
Radiation | Protocol: MIRAS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. all: 37249 / Num. obs: 38099 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2 / Num. unique all: 5397 / Rsym value: 0.157 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 34.5 Å / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.157 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2→14.85 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.4041 Å2 / ksol: 0.45023 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→14.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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