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- PDB-8ezf: A tethered niacin-derived pincer complex with a nickel-carbon or ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ezf | |||||||||
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Title | A tethered niacin-derived pincer complex with a nickel-carbon or sulfite-carbon bond in lactate racemase R98A/R100A variant | |||||||||
![]() | Lactate racemase | |||||||||
![]() | ISOMERASE / Catalytic activity / isomerase activity / racemase and epimerase activity racemase acting on hydroxy acids and derivatives / metal ion binding | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gatreddi, S. / Hausinger, R.P. / Hu, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor. Authors: Gatreddi, S. / Sui, D. / Hausinger, R.P. / Hu, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ezhC ![]() 8eziC ![]() 5huqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 47153.289 Da / Num. of mol.: 1 / Mutation: R98A, R100A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larA, lp_0104 / Production host: ![]() |
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-Non-polymers , 7 types, 194 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ENJ.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ENJ.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-ENJ / ( | #6: Chemical | ChemComp-NI / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Sodium HEPES/MOPS (pH 7.5), 60 mM Magnesium chloride hexahydrate, 60 mM Calcium chloride dihydrate, 20% Ethylene glycol and 10% PEG 8000 |
-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: Apr 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→37.97 Å / Num. obs: 23345 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.079 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1921 / Rpim(I) all: 0.45 / % possible all: 99.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5HUQ Resolution: 2.15→37.97 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.97 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.43 Å2 / Biso mean: 27.6493 Å2 / Biso min: 9.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→37.97 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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