+Open data
-Basic information
Entry | Database: PDB / ID: 6n3i | ||||||
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Title | Crystal structure of a double Trp XylE mutants (G58W/L315W) | ||||||
Components | D-xylose transporter | ||||||
Keywords | TRANSPORT PROTEIN / sugar transporter | ||||||
Function / homology | Function and homology information D-xylose:proton symporter activity / 2-alkenal reductase [NAD(P)+] activity / D-xylose transmembrane transport / 2-alkenal reductase [NAD(P)+] / transmembrane transporter activity / transmembrane transport / membrane => GO:0016020 / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å | ||||||
Authors | Jiang, X. / Wu, J.P. / Yan, N. | ||||||
Citation | Journal: Cell Discov / Year: 2019 Title: Engineered XylE as a tool for mechanistic investigation and ligand discovery of the glucose transporters GLUTs. Authors: Jiang, X. / Wu, J. / Ke, M. / Zhang, S. / Yuan, Y. / Lin, J.Y. / Yan, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n3i.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n3i.ent.gz | 158.1 KB | Display | PDB format |
PDBx/mmJSON format | 6n3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/6n3i ftp://data.pdbj.org/pub/pdb/validation_reports/n3/6n3i | HTTPS FTP |
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-Related structure data
Related structure data | 4gbzS S: Starting model for refinement |
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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
#1: Protein | Mass: 56770.914 Da / Num. of mol.: 1 / Mutation: G58W, L315W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: xylE, A6581_03910, A8C65_05810, A8G17_02365, A9R57_24335, ACU57_23655, AM266_00125, APT13_02355, ARC77_17295, AU473_00570, AUQ13_09605, AXA56_02835, BET08_27805, BHS87_22560, BIZ41_02050, BJJ90_ ...Gene: xylE, A6581_03910, A8C65_05810, A8G17_02365, A9R57_24335, ACU57_23655, AM266_00125, APT13_02355, ARC77_17295, AU473_00570, AUQ13_09605, AXA56_02835, BET08_27805, BHS87_22560, BIZ41_02050, BJJ90_24840, BTQ04_08325, BUE81_27360, BW690_24570, BWP17_09190, BZL31_21205, C4J69_17240, C5N07_20120, C9E25_05830, CR539_01970, CVH05_05200, DNQ41_01650, EC3234A_77c00210, ECs5014, EL75_4158, ERS085365_03771, ERS085383_01436, ERS085404_01231, ERS085416_00617, ERS139211_03640, ERS150873_01173, NCTC11022_04351, NCTC13127_06094, NCTC8500_05257, NCTC9010_04850, NCTC9037_04731, NCTC9045_05486, NCTC9058_02196, NCTC9060_03761, NCTC9062_03497, NCTC9110_04439, NCTC9701_04938, NCTC9969_04869, PGD_03203, RK56_017160, SAMEA3472067_03745, SAMEA3472080_00244, SAMEA3484427_03815, SAMEA3484429_02460, SAMEA3752557_02204, SAMEA3752559_00300, SAMEA3753093_02732, SAMEA3753106_03785, SAMEA3753300_00801, SAMEA3753391_00781, SAMEA3753397_01641 Production host: Escherichia coli (E. coli) References: UniProt: C3SHS4, UniProt: P0AGF4*PLUS, 2-alkenal reductase [NAD(P)+] |
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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: 4 Å3/Da / Density % sol: 69.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M NaCl, 0.1 M Li2SO4, 0.1 M MES pH6.5, 30% PEG400 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.69→40 Å / Num. obs: 10052 / % possible obs: 98.3 % / Redundancy: 5.5 % / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 3.7→3.83 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GBZ Resolution: 3.69→35.597 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.99 / 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 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.69→35.597 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.394 Å / Origin y: -15.4176 Å / Origin z: -2.9314 Å
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Refinement TLS group | Selection details: all |