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- PDB-7ris: Crystal structure of RPA3624, a beta-propeller lactonase from Rho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ris | ||||||
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Title | Crystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound phosphate | ||||||
![]() | Beta-propeller lactonase | ||||||
![]() | HYDROLASE / gamma-valerolactone | ||||||
Function / homology | gluconolactonase / gluconolactonase activity / Senescence marker protein-30 (SMP-30) / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / Six-bladed beta-propeller, TolB-like / metal ion binding / PHOSPHATE ION / Possible gluconolactonase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bingman, C.A. / Hall, B.W. / Smith, R.W. / Fox, B.G. / Donohue, T.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A broad specificity beta-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including gamma-valerolactone. Authors: Hall, B.W. / Bingman, C.A. / Fox, B.G. / Noguera, D.R. / Donohue, T.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 | ![]() | 209 KB | Display | ![]() |
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PDB format | ![]() | 139.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.3 KB | Display | ![]() |
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Full document | ![]() | 1003.2 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rizC ![]() 8djfC ![]() 8djzC ![]() 8dk0C 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32915.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-98 / CGA009 / Gene: RPA3624 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Crystals were grown in a MRC SD2 microplate, set with a TTP Labtech Mosquito crystallization robot. In the crystallization experiment leading to the crystal used for data collection, 200 nL ...Details: Crystals were grown in a MRC SD2 microplate, set with a TTP Labtech Mosquito crystallization robot. In the crystallization experiment leading to the crystal used for data collection, 200 nL of protein solution at 10.5 mg/mL was combined with 250 nL reservoir solution, composed of 20% PEG3350, 0.2M CaCl2, 0.1M bistris buffer pH 6.5. Crystals were cryopreserved by soaking in reservoir solution supplemented to 30% PEG3350 and immersion in liquid nitrogen |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03329 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→35.74 Å / Num. obs: 24269 / % possible obs: 99.62 % / Redundancy: 19.7 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08686 / Rpim(I) all: 0.02012 / Rrim(I) all: 0.08923 / Net I/σ(I): 20.07 |
Reflection shell | Resolution: 1.72→1.782 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.4783 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 2381 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.3297 / Rrim(I) all: 1.511 / % possible all: 99.29 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 38.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→35.74 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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