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- PDB-3m0y: Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3m0y | ||||||
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Title | Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant S329A in complex with L-rhamnose | ||||||
![]() | L-rhamnose isomerase | ||||||
![]() | ISOMERASE / BETA/ALPHA BARREL / HOMO-TETRAMER / METAL-BINDING PROTEIN / TIM barrel | ||||||
Function / homology | ![]() L-rhamnose isomerase activity / L-lyxose metabolic process / rhamnose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshida, H. / Takeda, K. / Izumori, K. / Kamitori, S. | ||||||
![]() | ![]() Title: Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of Pseudomonas stutzeri L-rhamnose isomerase Authors: Yoshida, H. / Takeda, K. / Izumori, K. / Kamitori, S. #1: ![]() Title: The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity Authors: Yoshida, H. / Yamada, M. / Ohyama, Y. / Takada, G. / Izumori, K. / Kamitori, S. #2: ![]() Title: Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures Authors: Yoshida, H. / Yamaji, M. / Ishii, T. / Izumori, K. / Kamitori, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 360.1 KB | Display | ![]() |
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PDB format | ![]() | 291.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.6 KB | Display | ![]() |
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Full document | ![]() | 490.8 KB | Display | |
Data in XML | ![]() | 72.1 KB | Display | |
Data in CIF | ![]() | 105.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m0hC ![]() 3m0lC ![]() 3m0mC ![]() 3m0vC ![]() 3m0xC ![]() 2hcvS 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: 47988.613 Da / Num. of mol.: 4 / Mutation: D150N, S329A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Sugar | ChemComp-RNS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 7-8% (w/v) polyethylene glycol 20000, 50mM MES pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 117176 / Num. obs: 117176 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HCV Resolution: 1.96→42.21 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 35876.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.6931 Å2 / ksol: 0.354778 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→42.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.08 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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