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- PDB-5nhd: Crystal structure of xylose isomerase from Piromyces E2 in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nhd | |||||||||
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Title | Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ ions and xylose | |||||||||
![]() | Xylose isomerase | |||||||||
![]() | ISOMERASE / TIM-barrel | |||||||||
Function / homology | ![]() xylose catabolic process to ethanol / xylose isomerase / xylose isomerase activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rozeboom, H.J. / Janssen, D.B. | |||||||||
![]() | ![]() Title: Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography. Authors: Lee, M. / Rozeboom, H.J. / de Waal, P.P. / de Jong, R.M. / Dudek, H.M. / Janssen, D.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 710 KB | Display | ![]() |
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PDB format | ![]() | 586.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.1 KB | Display | ![]() |
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Full document | ![]() | 526 KB | Display | |
Data in XML | ![]() | 78.1 KB | Display | |
Data in CIF | ![]() | 118.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nh4C ![]() 5nh5C ![]() 5nh6C ![]() 5nh7C ![]() 5nh8C ![]() 5nh9C ![]() 5nhaC ![]() 5nhbC ![]() 5nhcC ![]() 5nheC ![]() 5nhmC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49458.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): pBR322 Ori and ampicillin resitance gene Production host: ![]() ![]() |
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-Sugars , 3 types, 19 molecules ![](data/chem/img/XLS.gif)
![](data/chem/img/XYP.gif)
![](data/chem/img/XYS.gif)
![](data/chem/img/XYP.gif)
![](data/chem/img/XYS.gif)
#3: Sugar | ChemComp-XLS / #4: Sugar | ChemComp-XYP / #5: Sugar | ChemComp-XYS / |
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-Non-polymers , 3 types, 1764 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NI / #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 13-15 % PEG3350, 10 mM NiCl2, 0.1 M Hepes pH 7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 9, 2014 |
Radiation | Monochromator: Helios MX Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→39.4 Å / Num. obs: 146916 / % possible obs: 91.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 5.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.067 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7031 / CC1/2: 0.719 / Rpim(I) all: 0.361 / % possible all: 87.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: D_1200004044 Resolution: 1.8→39.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.947 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.449 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→39.4 Å
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Refine LS restraints |
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