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Yorodumi- PDB-1xgn: METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xgn | ||||||
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Title | METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS | ||||||
Components | METHIONINE AMINOPEPTIDASEMethionyl aminopeptidase | ||||||
Keywords | AMINOPEPTIDASE / HYPERTHERMOPHILE | ||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Tahirov, T.H. / Tsukihara, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 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: Journal: Acta Crystallogr.,Sect.D / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xgn.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xgn.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/1xgn ftp://data.pdbj.org/pub/pdb/validation_reports/xg/1xgn | HTTPS FTP |
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-Related structure data
Related structure data | 1xgmSC 1xgoC 1xgsC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.451342, 0.868787, -0.203715), Vector: |
-Components
#1: Protein | Mass: 32888.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TWO COBALT IONS IN ACTIVE SITE / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P56218, methionyl aminopeptidase #2: Chemical | ChemComp-CO / #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: 3.38 Å3/Da / Density % sol: 63.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 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 0.6% PROPANOL ...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 0.6% PROPANOL AND 1.6% PEG400 IN 0.1 M SODIUM HEPES BUFFER AT PH 7.5, THEN EQUILIBRATED AGAINST RESERVOIR SOLUTION. PH range: 4.5-7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 4.5 / Method: vapor diffusion, sitting dropDetails: Tahirov, T.H., (1997) Acta Crystallogr.,Sect.D, 53, 798. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 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: 2.9→50 Å / Num. obs: 17502 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 2.81 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.9→3.03 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.1 / % possible all: 62.7 |
Reflection | *PLUS Num. measured all: 91220 |
Reflection shell | *PLUS % possible obs: 62.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MONOCLINIC CRYSTAL FORM, PDB ENTRY 1XGM Resolution: 2.9→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 Details: PARAMETER AND TOPOLOGY FILES ARE MODIFIED TO INCLUDE THE COBALT IONS IN THE REFINEMENT.
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Displacement parameters | Biso mean: 37.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.34 |