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- PDB-1s5m: Xylose Isomerase in Substrate and Inhibitor Michaelis States: Ato... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s5m | ||||||
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Title | Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift | ||||||
![]() | Xylose isomerase | ||||||
![]() | ISOMERASE / xylose isomerase / hydride shift / atomic resolution / tim barrel | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fenn, T.D. / Ringe, D. / Petsko, G.A. | ||||||
![]() | ![]() Title: Xylose isomerase in substrate and inhibitor michaelis States: atomic resolution studies of a metal-mediated hydride shift(,). Authors: Fenn, T.D. / Ringe, D. / Petsko, G.A. | ||||||
History |
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Remark 999 | According to the author, the Swiss-Prot sequence (accession P15587)contains an error at position ... According to the author, the Swiss-Prot sequence (accession P15587)contains an error at position 175. Thr175 should be Ile175, however, the conflict is not yet noted in Swiss-Prot entry P15587. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.3 KB | Display | ![]() |
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PDB format | ![]() | 210.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1s5nC ![]() 1xyaS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 42856.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: XYLA / Plasmid: pX15 / Production host: ![]() ![]() | ||||
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#2: Sugar | ChemComp-GLC / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.21 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.1M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 398K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC / Detector: CCD / Details: MIRROR | |||||||||
Radiation | Monochromator: DOUBLE CRYSTAL SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 0.98→50 Å / Num. all: 229134 / Num. obs: 212189 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.1 | |||||||||
Reflection shell | Resolution: 0.98→1.02 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.3 / % possible all: 83.4 | |||||||||
Reflection shell | *PLUS % possible obs: 83.4 % / Num. unique obs: 20308 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: STREPTOMYCES OLIVOCHROMOGENES XYLOSE ISOMERASE - PDB ID 1XYA Resolution: 0.98→50 Å / Num. parameters: 33226 / Num. restraintsaints: 43898 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.3%
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Refine analyze | Num. disordered residues: 58 / Occupancy sum hydrogen: 2924.75 / Occupancy sum non hydrogen: 3448.32 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.98→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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