+Open data
-Basic information
Entry | Database: PDB / ID: 6yak | ||||||
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Title | Split gene transketolase, active alpha2beta2 heterotetramer | ||||||
Components |
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Keywords | TRANSFERASE / Hyperthermophilic / split-gene transketolase / thermal stability / industrial applications | ||||||
Function / homology | Chem-8EL / (2S)-2-hydroxybutanedioic acid / D-MALATE Function and homology information | ||||||
Biological species | Carboxydothermus hydrogenoformans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Isupov, M.N. / Littlechild, J.A. / James, P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Front Microbiol / Year: 2020 Title: A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans : Structure and Biochemical Characterization. Authors: James, P. / Isupov, M.N. / De Rose, S.A. / Sayer, C. / Cole, I.S. / 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 | 6yak.cif.gz | 506.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yak.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yak_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6yak_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6yak_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 6yak_validation.cif.gz | 95.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/6yak ftp://data.pdbj.org/pub/pdb/validation_reports/ya/6yak | HTTPS FTP |
-Related structure data
Related structure data | 6yajC 1qgdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.3708998 / 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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Protein , 2 types, 4 molecules AAACCCBBBDDD
#1: Protein | Mass: 33917.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria) Production host: Escherichia coli (E. coli) #2: Protein | Mass: 36013.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria) Production host: Escherichia coli (E. coli) |
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-Non-polymers , 6 types, 1450 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MLT / #6: Chemical | ChemComp-LMR / ( #7: Chemical | ChemComp-CL / #8: 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: 2.37 Å3/Da / Density % sol: 48.17 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / Details: 2.1 M DL-malic acid pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→60.878 Å / Num. obs: 288149 / % possible obs: 97.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 1 / Rrim(I) all: 0.056 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.34→1.36 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 11686 / CC1/2: 0.266 / Rrim(I) all: 1.619 / % possible all: 81.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qgd Resolution: 1.34→60.87 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.045 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→60.87 Å
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Refine LS restraints |
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LS refinement shell |
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