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- PDB-1xgs: METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xgs | ||||||
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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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.5 KB | Display | ![]() |
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PDB format | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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: (-0.956232, -0.267113, 0.11946), Vector: |
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Components
#1: Protein | Mass: 32888.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CONTAIN TWO COBALT IONS IN ACTIVE SITE / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.9 % Description: DATA WERE COLLECTED USING 2 DEGREE OSCILLATION. LOW-HUMIDITY FORM CRYSTAL FORM USED FOR DATA COLLECTION WAS OBTAINED BY WATER-MEDIATED TRANSFORMATION OF NATIVE MONOCLINIC PFMAP CRYSTAL. | ||||||||||||||||||||||||||||||||||||
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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. OBTAINED CRYSTALS WERE TRANSFORMED TO LOW-HUMIDITY FORM BY CONTROLLING THE RELATIVE HUMIDITY USING THE SATURATED SALT SOLUTIONS (AMMONIUM SULFATE AT LAST STAGE). PH range: 4.5-8.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tahirov, T., (1998) J. Struct. Biol., 121, 68. / pH: 4.5 | ||||||||||||||||||||||||||||||||||||
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: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. obs: 49955 / % possible obs: 84.6 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.6 / % possible all: 62.4 |
Reflection | *PLUS Num. measured all: 192734 |
Reflection shell | *PLUS % possible obs: 62.4 % |
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Processing
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Refinement | Method to determine structure: RIGID-BODY REFINEMENT Starting model: STRUCTURE OF NATIVE MONOCLINIC PFMAP CRYSTAL DETERMINED BY MIR METHOD Resolution: 1.75→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: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.83 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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