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- PDB-4gji: 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: 4gji | ||||||
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Title | Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with L-rhamnopyranose | ||||||
![]() | L-rhamnose isomerase | ||||||
![]() | ISOMERASE / Tim Barrel / Sugar binding / Metal binding | ||||||
Function / homology | ![]() L-rhamnose isomerase activity / L-lyxose metabolic process / rhamnose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshida, H. / Kamitori, S. | ||||||
![]() | ![]() Title: Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. Authors: Yoshida, H. / Yoshihara, A. / Teraoka, M. / Yamashita, S. / 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. #3: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 379.4 KB | Display | ![]() |
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PDB format | ![]() | 303.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4gjjC ![]() 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 47980.570 Da / Num. of mol.: 4 / Fragment: TIM barrel / Mutation: D150N, H101N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 11 molecules ![](data/chem/img/RNS.gif)
![](data/chem/img/RAM.gif)
![](data/chem/img/RM4.gif)
![](data/chem/img/RAM.gif)
![](data/chem/img/RM4.gif)
#2: Sugar | ChemComp-RNS / #3: Sugar | ChemComp-RAM / #5: Sugar | |
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-Non-polymers , 2 types, 1974 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | RM4 501 AND RNS 502 ARE IN ALTERNATE CONFORMATI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 7-8% (w/v) PEG 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 270 / Detector: CCD / Date: Jun 17, 2011 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 182769 / Num. obs: 182769 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.9 / Num. unique all: 9074 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HCV Resolution: 1.7→31.48 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 157137.35 / 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: 61.0989 Å2 / ksol: 0.391326 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→31.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
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Xplor file |
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