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- PDB-1xgo: METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xgo | ||||||
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Title | METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS | ||||||
![]() | METHIONINE AMINOPEPTIDASE | ||||||
![]() | AMINOPEPTIDASE / HYPERTHERMOPHILE | ||||||
Function / homology | ![]() initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / proteolysis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tahirov, T.H. / Tsukihara, T. | ||||||
![]() | ![]() Title: Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. Authors: Tahirov, T.H. / Oki, H. / Tsukihara, T. / Ogasahara, K. / Yutani, K. / Ogata, K. / Izu, Y. / Tsunasawa, S. / Kato, I. #1: ![]() Title: Crystallization and Preliminary X-Ray Analysis of Methionine Aminopeptidase from the Hyperthermophilic Bacterium Pyrococcus Furiosus Authors: Tahirov, T.H. / Oki, H. / Tsukihara, T. / Ogasahara, K. / Izu, Y. / Tsunasawa, S. / Kato, I. / Yutani, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.5 KB | Display | ![]() |
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PDB format | ![]() | 51.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.2 KB | Display | ![]() |
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Full document | ![]() | 448.8 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xgmSC ![]() 1xgnC ![]() 1xgsC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 32888.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: TWO COBALT IONS IN ACTIVE SITE REMOVED BY THE REDUCTION OF PH TO 2.6 Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.412 Å3/Da / Density % sol: 77.4 % | |||||||||||||||
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Crystal grow | pH: 2.6 Details: PROTEIN SOLUTION CONTAINING 16 MG/ML PFMAP, 2 MM COCL2 AND 30 MM L-METHIONINE IN 20 MM POTASSIUM ACETATE AT PH4.5 WAS MIXED WITH EQUAL AMOUNT OF RESERVOIR SOLUTION CONTAINING 10% PEG6000 AND ...Details: PROTEIN SOLUTION CONTAINING 16 MG/ML PFMAP, 2 MM COCL2 AND 30 MM L-METHIONINE IN 20 MM POTASSIUM ACETATE AT PH4.5 WAS MIXED WITH EQUAL AMOUNT OF RESERVOIR SOLUTION CONTAINING 10% PEG6000 AND 2.0 M SODIUM CHLORIDE AT PH 2.6, THEN EQUILIBRATED AGAINST RESERVOIR SOLUTION. PH range: 2.6-4.5 | |||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 7571 / % possible obs: 84.3 % / Observed criterion σ(I): 1 / Redundancy: 3.65 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.5→3.63 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.9 / % possible all: 64.9 |
Reflection | *PLUS Num. measured all: 59765 |
Reflection shell | *PLUS % possible obs: 64.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MONOCLINIC CRYSTAL FORM, PDB ENTRY 1XGM Resolution: 3.5→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 31.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.66 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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