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Yorodumi- PDB-7b0m: Sugar transaminase from a metagenome collected from troll oil fie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b0m | ||||||
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Title | Sugar transaminase from a metagenome collected from troll oil field production water | ||||||
Components | Sugar aminotransferase | ||||||
Keywords | TRANSFERASE / aminotransferase / thermostability / catalysis | ||||||
Function / homology | Aminotransferase, LLPSF_NHT_00031 family / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / DI(HYDROXYETHYL)ETHER / Sugar aminotransferase Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Littlechild, J.A. / De Rose, S.A. / Isupov, M.N. / Sayer, C. / Karki, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Sugar transaminases from hot environments Authors: James, P. / Littlechild, J.A. / De Rose, S.A. / Isupov, M.N. / Karki, S. / Tabji, A.B. / Garcia-Moyano, A. / Birkeland, N.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b0m.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b0m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b0m ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b0m | HTTPS FTP |
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-Related structure data
Related structure data | 7b0dC 3bn1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4282117 / Data set type: diffraction image 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
#1: Protein | Mass: 42307.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: A0A5Q0MTV0 | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PG4 / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.06 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 4.2 Details: 0.2 M Lithium Sulfate,0.1 M Phosphate, 20% w/v PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→59.37 Å / Num. obs: 84599 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 8.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 8.3 % / Rmerge(I) obs: 2.873 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4170 / CC1/2: 0.282 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BN1 Resolution: 1.43→59.37 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.565 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.06 Details: Hydrogens have been added in their riding positions
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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: 34.673 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→59.37 Å
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Refine LS restraints |
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LS refinement shell |
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