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- PDB-3m21: Crystal structure of DmpI from Helicobacter pylori Determined to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m21 | ||||||
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Title | Crystal structure of DmpI from Helicobacter pylori Determined to 1.9 Angstroms resolution | ||||||
![]() | Probable tautomerase HP_0924 | ||||||
![]() | ISOMERASE / 4-oxalocrotonate tautomerase / catalytic proline / hexamer / beta-alpha-beta | ||||||
Function / homology | ![]() Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / : / isomerase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hackert, M.L. / Whitman, C.P. / Almrud, J.J. / Dasgupta, R. / Kern, A.D. / Czerwinski, R.M. | ||||||
![]() | ![]() Title: Kinetic and structural characterization of DmpI from Helicobacter pylori and Archaeoglobus fulgidus, two 4-oxalocrotonate tautomerase family members. Authors: Almrud, J.J. / Dasgupta, R. / Czerwinski, R.M. / Kern, A.D. / Hackert, M.L. / Whitman, C.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.5 KB | Display | ![]() |
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PDB format | ![]() | 68.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.6 KB | Display | ![]() |
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Full document | ![]() | 462.2 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ormC ![]() 3m20C ![]() 1bjpS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 7389.381 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O25581, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Crystals were grown using a well solution of 25% t-butanol, 0.1M Na Citrate, pH 5.5. Protein was 20 mg/ml in 50 mM NaH2PO4, pH 7.3. 5 microliters of well solution was mixed with 5 ...Details: Crystals were grown using a well solution of 25% t-butanol, 0.1M Na Citrate, pH 5.5. Protein was 20 mg/ml in 50 mM NaH2PO4, pH 7.3. 5 microliters of well solution was mixed with 5 microliters of protein and vapor equilibrated using sitting drop, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 108 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2000 / 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: 1.85→30 Å / Num. obs: 27541 / % possible obs: 89.3 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.044 / Χ2: 0.944 / Net I/σ(I): 22.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BJP Resolution: 1.9→30 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 63 / Stereochemistry target values: mlf
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Solvent computation | Bsol: 59.282 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.59 Å2 / Biso mean: 33.18 Å2 / Biso min: 13.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.94 Å / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.281 | ||||||||||||||||||||||||||||
Xplor file |
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