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- PDB-1m1b: Crystal Structure of Phosphoenolpyruvate Mutase Complexed with Su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m1b | ||||||
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Title | Crystal Structure of Phosphoenolpyruvate Mutase Complexed with Sulfopyruvate | ||||||
![]() | PHOSPHOENOLPYRUVATE PHOSPHOMUTASE | ||||||
![]() | ISOMERASE / phosphoenolpyruvate mutase / PEP mutase / sulfopyruvate | ||||||
Function / homology | ![]() phosphoenolpyruvate mutase / phosphoenolpyruvate mutase activity / organic phosphonate biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, S. / Lu, Z. / Jia, Y. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
![]() | ![]() Title: Dissociative phosphoryl transfer in PEP mutase catalysis: structure of the enzyme/sulfopyruvate complex and kinetic properties of mutants. Authors: Liu, S. / Lu, Z. / Jia, Y. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.8 KB | Display | ![]() |
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PDB format | ![]() | 101 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.2 KB | Display | ![]() |
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Full document | ![]() | 480 KB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pymS S: Starting model for refinement |
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Similar 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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Components
#1: Protein | Mass: 32954.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, glycerol, magnesium chloride, Hepes, sulfopyruvate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 8 / PH range high: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 2001 / Details: mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→26.5 Å / Num. all: 25261 / Num. obs: 21045 / % possible obs: 83.3 % / Observed criterion σ(F): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 3.7 / % possible all: 64.9 |
Reflection | *PLUS Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 64.9 % / Rmerge(I) obs: 0.244 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PYM Resolution: 2.25→26.5 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→26.5 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 6 % / Rfactor obs: 0.185 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.179 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.5 |