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- PDB-3hk9: Crystal structure of uronate isomerase from Bacillus halodurans c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hk9 | ||||||
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Title | Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Glucuronate | ||||||
![]() | Uronate isomerase | ||||||
![]() | ISOMERASE / uronate isomerase / D-Glucuronate / Mechanism of the reaction | ||||||
Function / homology | uronate isomerase, domain 2, chain A / uronate isomerase, domain 2, chain A / Metal-dependent hydrolase / Orthogonal Bundle / Mainly Alpha / metal ion binding / CARBONATE ION / D-glucuronic acid / BH0493 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Fedorov, E.V. / Nguyen, T.T. / Raushel, F.M. / Almo, S.C. | ||||||
![]() | ![]() Title: The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily. Authors: Nguyen, T.T. / Fedorov, A.A. / Williams, L. / Fedorov, E.V. / Li, Y. / Xu, C. / Almo, S.C. / Raushel, F.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1019.4 KB | Display | ![]() |
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PDB format | ![]() | 847.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 569.9 KB | Display | ![]() |
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Full document | ![]() | 655.5 KB | Display | |
Data in XML | ![]() | 193.6 KB | Display | |
Data in CIF | ![]() | 256.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hk5C ![]() 3hk7C ![]() 3hk8C ![]() 3hkaC ![]() 2q08S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 24 molecules ABCDEFGHIJKL![](data/chem/img/REL.gif)
![](data/chem/img/REL.gif)
#1: Protein | Mass: 50006.852 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-REL / |
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-Non-polymers , 4 types, 1852 molecules ![](data/chem/img/CO3.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CO3 / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.2M Ammonium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 2007 / Details: mirrors |
Radiation | Monochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 404122 / Num. obs: 404122 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.074 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2Q08 Resolution: 2.1→24.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1778514.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.3742 Å2 / ksol: 0.361085 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
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Xplor file |
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