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Yorodumi- PDB-5qqu: PanDDA analysis group deposition -- Crystal Structure of human AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qqu | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z1348371854 | ||||||
Components | 5-aminolevulinate synthase, erythroid-specific, mitochondrialAminolevulinic acid synthase | ||||||
Keywords | TRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
Function / homology | Function and homology information 5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / intracellular oxygen homeostasis / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / erythrocyte development / erythrocyte differentiation / pyridoxal phosphate binding ...5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / intracellular oxygen homeostasis / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / erythrocyte development / erythrocyte differentiation / pyridoxal phosphate binding / intracellular iron ion homeostasis / mitochondrial inner membrane / response to hypoxia / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.55 Å | ||||||
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. ...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. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qqu.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qqu.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 5qqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/5qqu ftp://data.pdbj.org/pub/pdb/validation_reports/qq/5qqu | 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 |
-Links
-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.) Homo sapiens (human) / Gene: ALAS2, ALASE, ASB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22557, 5-aminolevulinate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.52 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.551→55.573 Å / Num. obs: 90137 / % possible obs: 94.8 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rpim(I) all: 0.045 / Rrim(I) all: 0.085 / Net I/σ(I): 10 / Num. measured all: 310163 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6hrh Resolution: 1.55→80.25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.4 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.125 / 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: 78.27 Å2 / Biso mean: 21.047 Å2 / Biso min: 6 Å2
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Refinement step | Cycle: final / Resolution: 1.55→80.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.549→1.589 Å / Total num. of bins used: 20
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