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- PDB-2orm: Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2orm | ||||||
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Title | Crystal Structure of the 4-Oxalocrotonate Tautomerase Homologue DmpI from Helicobacter pylori. | ||||||
![]() | Probable tautomerase HP0924 | ||||||
![]() | ISOMERASE / homohexamer / 4-OT / 4-Oxalocrotonate Tautomerase Homologue | ||||||
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. / Czerwinski, R.M. / Kern, A.D. | ||||||
![]() | ![]() 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 | ![]() | 85.3 KB | Display | ![]() |
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PDB format | ![]() | 65.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.1 KB | Display | ![]() |
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Full document | ![]() | 465.4 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m20C ![]() 3m21C ![]() 1bjpS S: Starting model for refinement C: citing same article ( |
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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: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees ...Details: 2 uL of protein (20 mg/mL) in 20mM phosphate buffer (pH 7.4) were mixed with 2 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400. This combined volume was equilibrated at 4 degrees Celcius against 50 uL of 0.2M CaCl2, 0.1M Hepes (pH 7.5), and 28% PEG 400 , VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50 |
-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 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.5 Å / Num. obs: 20368 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 5.94 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.096 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.476 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BJP Resolution: 2.1→24.5 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: RANDOM / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.026
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