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Yorodumi- PDB-7nzq: D-lyxose isomerase from the hyperthermophilic archaeon Thermofilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nzq | ||||||
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Title | D-lyxose isomerase from the hyperthermophilic archaeon Thermofilum sp complexed with D-mannose | ||||||
Components | D-lyxose/D-mannose family sugar isomerase | ||||||
Keywords | ISOMERASE / Complex / thermostability / biocatalysis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermofilum sp. ex4484_79 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | De Rose, S.A. / Isupov, M.N. / Littlechild, J.A. / Schoenheit, P. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Front Bioeng Biotechnol / Year: 2021 Title: Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp. Authors: De Rose, S.A. / Kuprat, T. / Isupov, M.N. / Reinhardt, A. / Schonheit, P. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nzq.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nzq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/7nzq ftp://data.pdbj.org/pub/pdb/validation_reports/nz/7nzq | HTTPS FTP |
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-Related structure data
Related structure data | 7nzoC 7nzpC 2y0oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
-Protein / Sugars , 2 types, 2 molecules AAA
#1: Protein | Mass: 23898.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermofilum sp. ex4484_79 (archaea) / Gene: B6U94_07925 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A256XLS3 |
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#2: Sugar | ChemComp-BMA / |
-Non-polymers , 5 types, 229 molecules
#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-MN / | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6 Details: 100 mM SPG ph 6.0, 25% w/v PEG 1500, 40 mM D-mannose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→37.692 Å / Num. obs: 29074 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 1.57→1.6 Å / Num. unique obs: 1425 / CC1/2: 0.277 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2y0o Resolution: 1.57→37.692 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.575 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.09 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.025 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→37.692 Å
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Refine LS restraints |
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LS refinement shell |
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