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Yorodumi- PDB-1xgm: METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xgm | ||||||
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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 / SYNCHROTRON / MIR / Resolution: 2.8 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 | 1xgm.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xgm.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 1xgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/1xgm ftp://data.pdbj.org/pub/pdb/validation_reports/xg/1xgm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.957964, -0.264121, 0.112007), 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: 2.39 Å3/Da / Density % sol: 48.8 % Description: THREE HEAVY-ATOM DERIVATIVES USED FOR STRUCTURE DETERMINATION WERE OBTAINED BY SOAKING OF NATIVE CRYSTALS IN BUFFER SOLUTION WITH 0.1 MM OF K2PTCL6, K3UO2F5, AND C6H5HGOCOCH3. THE ...Description: THREE HEAVY-ATOM DERIVATIVES USED FOR STRUCTURE DETERMINATION WERE OBTAINED BY SOAKING OF NATIVE CRYSTALS IN BUFFER SOLUTION WITH 0.1 MM OF K2PTCL6, K3UO2F5, AND C6H5HGOCOCH3. THE DERIVATIVES DIFFRACTED TO RESOLUTION OF 3.5 A. NCS RESTRAINTS WERE APPLIED FOR ALL NONSOLVENT ATOMS IN ALL STAGES OF REFINEMENT EXCEPT THE LAST STEP OF POSITIONAL AND B-VALUE REFINEMENT IN WHICH THE NCS RESTRAINTS WERE RELEASED FROM RESIDUES 204 - 265. | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 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 20% ETHANOL IN ...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 20% ETHANOL IN 0.1 M TRIS BUFFER AT PH 8.5, THEN EQUILIBRATED AGAINST RESERVOIR SOLUTION. PH range: 4.5-8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / 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: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 12285 / % possible obs: 80.3 % / Observed criterion σ(I): 1 / Redundancy: 2.95 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.1 / % possible all: 51.9 |
Reflection | *PLUS Num. measured all: 42890 |
Reflection shell | *PLUS % possible obs: 51.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→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: 36.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.93 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: 0.38 |