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Yorodumi- PDB-7fir: The crystal structure of beta-1,2-mannobiose phosphorylase in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fir | ||||||
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Title | The crystal structure of beta-1,2-mannobiose phosphorylase in complex with 1,4-mannobiose | ||||||
Components | Beta-1,2-mannobiose phosphorylase | ||||||
Keywords | TRANSFERASE / Mannobiose / phosphorylase / thermoanaerobacter / crystallization / complex structure | ||||||
Function / homology | beta-1,2-mannobiose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / GDP-mannose biosynthetic process / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / TRIETHYLENE GLYCOL / Beta-1,2-mannobiose phosphorylase Function and homology information | ||||||
Biological species | Thermoanaerobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dai, L. / Chang, Z. / Yang, J. / Liu, W. / Yang, Y. / Chen, C.-C. / Zhang, L. / Huang, J. / Sun, Y. / Guo, R.-T. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Structural investigation of a thermostable 1,2-beta-mannobiose phosphorylase from Thermoanaerobacter sp. X-514. Authors: Dai, L. / Chang, Z. / Yang, J. / Liu, W. / Yang, Y. / Chen, C.C. / Zhang, L. / Huang, J.W. / Sun, Y. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fir.cif.gz | 291.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fir.ent.gz | 231 KB | Display | PDB format |
PDBx/mmJSON format | 7fir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/7fir ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fir | HTTPS FTP |
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-Related structure data
Related structure data | 7fipC 7fiqC 7fisC 5b0rS 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
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 35856.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter sp. (strain X514) (bacteria) Strain: X514 / Gene: Teth514_1789 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B0K2C3, beta-1,2-mannobiose phosphorylase #2: Polysaccharide | alpha-L-gulopyranose-(1-4)-alpha-L-allopyranose Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 1292 molecules
#3: Chemical | ChemComp-PGE / | ||||
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#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
-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: 2.89 Å3/Da / Density % sol: 57.43 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / Details: 10 mM ZnCl2, 28% PEG3350, 160 mM Tris-HCl pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Nov 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→36.29 Å / Num. obs: 161051 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3738 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5b0r Resolution: 2.2→36.29 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.39 Å2 / Biso mean: 27.0358 Å2 / Biso min: 5.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→36.29 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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