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- PDB-6ovl: 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ovl | ||||||
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Title | 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP | ||||||
![]() | Glyoxylate/hydroxypyruvate reductase A | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vuksanovic, N. / Silvaggi, N.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 2.1 Angstrom structure of wild type Glyoxylate/Hydroxypyruvate reductase A from Escherichia Coli in complex with glyoxylate and NADP Authors: Vuksanovic, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.8 KB | Display | ![]() |
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PDB format | ![]() | 170.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6oxnC ![]() 6p35C ![]() 3kboS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36186.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: W8T4J3, UniProt: P75913*PLUS, ![]() ![]() |
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-Non-polymers , 7 types, 288 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/GLV.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/GLV.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / ![]() | ||||||||||
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#3: Chemical | ![]() #4: Chemical | ChemComp-NAP / | ![]() #5: Chemical | ChemComp-GLV / | ![]() #6: Chemical | ChemComp-K / | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.4 M sodium phosphate monobasic/ potassium phosphate dibasic, 5 mM NADP, 100 mM sodium glyoxylate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→36.73 Å / Num. obs: 41974 / % possible obs: 99.09 % / Redundancy: 16.3 % / Biso Wilson estimate: 27.6828559215 Å2 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 3924 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3KBO Resolution: 2.1→36.73 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.86 / 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: 2.1→36.73 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: -18.4953 Å / Origin y: 63.8768 Å / Origin z: -18.8906 Å
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Refinement TLS group | Selection details: all |