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- PDB-1xlm: D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xlm | ||||||
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Title | D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL | ||||||
![]() | D-XYLOSE ISOMERASE | ||||||
![]() | ISOMERASE / AL / SUBSTRATE INDUCED METAL ION MOVEMENT / XYLOSE METABOLISM / PENTOSE SHUNT | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gerczei, T. / Bocskei, Z.S. / Szabo, E. / Naray-Szabo, G. / Asboth, B. | ||||||
![]() | ![]() Title: Structure determination and refinement of the Al3+ complex of the D254,256E mutant of Arthrobacter D-xylose isomerase at 2.40 A resolution. Further evidence for inhibitor-induced metal ion movement. Authors: Gerczei, T. / Bocskei, Z. / Szabo, E. / Asboth, B. / Naray-Szabo, G. #1: ![]() Title: Role of Electrostatics at the Catalytic Metal Binding Site in Xylose Isomerase Action: Ca(2+)-Inhibition and Metal Competence in the Double Mutant D254E/D256E Authors: Fuxreiter, M. / Bocskei, Z. / Szeibert, A. / Szabo, E. / Dallmann, G. / Naray-Szabo, G. / Asboth, 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 | ![]() | 160.7 KB | Display | ![]() |
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PDB format | ![]() | 127.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 42 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xlaS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.076426, -0.997075, -0.001045), Vector: |
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Components
#1: Protein | Mass: 43237.219 Da / Num. of mol.: 2 / Mutation: D254E, D256E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | #3: Chemical | ChemComp-AL / #4: 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: 53 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 0.75 M (NH4)2SO4, 1.50 MM THYMOL, 0.05 TRIS, PH 7.0, THEN SOAKED INTO A SOLUTION CONTAINING 5 MM AL3+, 1.5 M XYLITOL, 1.50 M (NH4)2SO4 AND 6.0 M THYMOL IN 1.50 ...Details: PROTEIN WAS CRYSTALLIZED FROM 0.75 M (NH4)2SO4, 1.50 MM THYMOL, 0.05 TRIS, PH 7.0, THEN SOAKED INTO A SOLUTION CONTAINING 5 MM AL3+, 1.5 M XYLITOL, 1.50 M (NH4)2SO4 AND 6.0 M THYMOL IN 1.50 M TRIS-HCL PH 8.0 FOR TWO DAYS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: NORMAL FOCUS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→8 Å / Num. obs: 32570 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.078 / Net I/σ(I): 4.87 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.164 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 142427 / Rmerge(I) obs: 0.1195 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XLA Resolution: 2.4→8 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 14.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 1.317 Å2 / Rms dev position: 0.017 Å / Weight Biso : 1 / Weight position: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.44 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2223 / Num. reflection obs: 108813 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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