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- PDB-3itv: 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: 3itv | ||||||
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Title | Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant S329K in complex with D-psicose | ||||||
![]() | L-rhamnose isomerase | ||||||
![]() | ISOMERASE / METAL-BINDING PROTEIN / BETA/ALPHA BARREL / HOMO-TETRAMER / 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. / Yamaji, M. / Ishii, T. / Izumori, K. / Kamitori, S. | ||||||
![]() | ![]() 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. #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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 377.4 KB | Display | ![]() |
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PDB format | ![]() | 301.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.7 KB | Display | ![]() |
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Full document | ![]() | 496.1 KB | Display | |
Data in XML | ![]() | 79.3 KB | Display | |
Data in CIF | ![]() | 121.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3itlC ![]() 3itoC ![]() 3ittC ![]() 3itxC ![]() 3ityC ![]() 3iudC ![]() 3iuhC ![]() 3iuiC ![]() 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: 48046.715 Da / Num. of mol.: 4 / Mutation: D150N, S329K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Sugar | ChemComp-PSJ / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 298 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 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 14, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 208180 / Num. obs: 208180 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 10.7 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HCV Resolution: 1.6→46.39 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 119219.74 / 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: 51.9613 Å2 / ksol: 0.375663 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→46.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Xplor file |
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