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- PDB-5qqt: PanDDA analysis group deposition -- Crystal Structure of human AL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5qqt | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z2856434834 | ||||||
![]() | 5-aminolevulinate synthase, erythroid-specific, mitochondrial![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. ...Bezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Brennan, P.E. / Yue, W.W. | ||||||
![]() | ![]() Title: PanDDA analysis group deposition Authors: Bezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / ...Authors: Bezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Brennan, P.E. / Yue, W.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.7 KB | Display | ![]() |
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PDB format | ![]() | 143.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002078 (25 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | human 5'-Aminolevulinate synthase erythroid-specific (ALAS2) screened against the DSi Poised Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | ![]() 6hrhS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 52250.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-NT7 / | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.2 M magnesium chloride, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 1.674→71.513 Å / Num. obs: 68893 / % possible obs: 93.9 % / Redundancy: 3.4 % / CC1/2: 0.994 / Rpim(I) all: 0.075 / Rrim(I) all: 0.141 / Net I/σ(I): 6.8 / Num. measured all: 235632 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6hrh Resolution: 1.67→80.19 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.561 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.18 Å2 / Biso mean: 21.653 Å2 / Biso min: 6.63 Å2
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Refinement step | Cycle: final / Resolution: 1.67→80.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.671→1.715 Å / Total num. of bins used: 20
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