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Open data
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Basic information
Entry | Database: PDB / ID: 6tzy | ||||||||||||
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Title | Crystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase | ||||||||||||
![]() | Nuclear elongation and deformation protein | ||||||||||||
![]() | HYDROLASE / Lipin / phosphatidic acid phosphatase / immunoglobulin-like / haloacid dehalogenase | ||||||||||||
Function / homology | ![]() phosphatidate phosphatase activity / triglyceride biosynthetic process / fatty acid catabolic process / cellular response to insulin stimulus / transcription coactivator activity / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Khayyo, V.I. / Airola, M.V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase Authors: Khayyo, V.I. / Hoffmann, R.M. / Wang, H. / Bell, J.A. / Burke, J.E. / Reue, K. / Airola, M.V. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 438.4 KB | Display | ![]() |
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PDB format | ![]() | 363 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.1 KB | Display | ![]() |
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Full document | ![]() | 384 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tzzS S: Starting model for refinement |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36734.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M Ca(NO3)2, 15% PEG 8,000, 0.1M MES pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.66→53.23 Å / Num. obs: 33662 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Net I/σ(I): 10 / Num. measured all: 235447 / Scaling rejects: 694 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TZZ Resolution: 3→52.05 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 30.89 / 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: 282.16 Å2 / Biso mean: 95.6948 Å2 / Biso min: 31.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→52.05 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 6.162 Å / Origin y: -20.539 Å / Origin z: 29.901 Å
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Refinement TLS group |
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