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Yorodumi- PDB-8tnf: Crystal structure of sulfohexulose-1-phosphate aldolase from Para... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tnf | ||||||
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Title | Crystal structure of sulfohexulose-1-phosphate aldolase from Paracoccus onubensis strain Merri | ||||||
Components | DUF2090 domain-containing protein | ||||||
Keywords | LYASE / sulfohexulose-1-phosphate aldolase | ||||||
Function / homology | : / 6-deoxy-6-sulfofructose-1-phosphate aldolase activity / 6-sulfoquinovose(1-) catabolic process / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase-type TIM barrel / DUF2090 domain-containing protein Function and homology information | ||||||
Biological species | Paracoccus onubensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lee, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: A patchwork pathway for catabolism degradation of the sulfosugar sulfofucose Authors: Li, J. / Lee, M. / Yang, S. / Lewis, J.M. / Herisse, M. / Pidot, S.J. / Scott, N.E. / Williams, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tnf.cif.gz | 508.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tnf.ent.gz | 419.9 KB | Display | PDB format |
PDBx/mmJSON format | 8tnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tnf_validation.pdf.gz | 510.1 KB | Display | wwPDB validaton report |
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Full document | 8tnf_full_validation.pdf.gz | 538.4 KB | Display | |
Data in XML | 8tnf_validation.xml.gz | 90.5 KB | Display | |
Data in CIF | 8tnf_validation.cif.gz | 125.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/8tnf ftp://data.pdbj.org/pub/pdb/validation_reports/tn/8tnf | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40151.359 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus onubensis (bacteria) / Strain: Merrie / Gene: D3P04_00185 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A418T8G4 #2: Water | ChemComp-HOH / | |
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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: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 0.2 M L-proline, 14-18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.98 Å / Num. obs: 121327 / % possible obs: 97.7 % / Redundancy: 1.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.077 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 5943 / CC1/2: 0.538 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.88 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.879 / SU R Cruickshank DPI: 0.45 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.412 / SU Rfree Blow DPI: 0.284 / SU Rfree Cruickshank DPI: 0.295
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Displacement parameters | Biso mean: 52.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.52 Å
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