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Open data
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Basic information
Entry | Database: PDB / ID: 7v3k | ||||||
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Title | crystal structure of MAJ1 | ||||||
![]() | Putative lipase | ||||||
![]() | LIPID BINDING PROTEIN | ||||||
Function / homology | Lipase EstA/Esterase EstB / Lipase (class 2) / lipid catabolic process / Alpha/Beta hydrolase fold / hydrolase activity / OLEIC ACID / Putative lipase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.H. / Cui, R.G. | ||||||
Funding support | 1items
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![]() | ![]() Title: crystal structure of MAJ1 Authors: Wang, Y.H. / Cui, R.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.6 KB | Display | ![]() |
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PDB format | ![]() | 196 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5h6gS S: Starting model for refinement |
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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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 8 molecules ACDB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 33031.879 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 597 molecules ![](data/chem/img/OLA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OLA / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 3.35 Å3/Da / Density % sol: 63.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20%PEG3350,200mM potassium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 60324 / % possible obs: 96.1 % / Redundancy: 9.6 % / Biso Wilson estimate: 34.92 Å2 / CC1/2: 0.917 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.109 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.49→2.54 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 2958 / Rpim(I) all: 0.311 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5H6G Resolution: 2.49→22.89 Å / SU ML: 0.3137 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7294 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: 37.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→22.89 Å
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Refine LS restraints |
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LS refinement shell |
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