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Yorodumi- PDB-5qr3: PanDDA analysis group deposition -- Crystal Structure of human AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qr3 | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z915492990 | ||||||
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 / erythrocyte development / heme biosynthetic process / erythrocyte differentiation / pyridoxal phosphate binding ...5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / intracellular oxygen homeostasis / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / erythrocyte development / heme biosynthetic process / erythrocyte differentiation / pyridoxal phosphate binding / mitochondrial inner membrane / intracellular iron ion homeostasis / response to hypoxia / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.71 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 | 5qr3.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qr3.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 5qr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/5qr3 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/5qr3 | 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
#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 | ChemComp-JO1 / | #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: 2.36 Å3/Da / Density % sol: 47.94 % |
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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: 1.71→48.499 Å / Num. obs: 81715 / % possible obs: 95 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 12.4 / Num. measured all: 281169 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.4 %
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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: 1.71→55.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.351 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.139 / 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: 95.29 Å2 / Biso mean: 27.251 Å2 / Biso min: 11.82 Å2
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Refinement step | Cycle: final / Resolution: 1.71→55.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.755 Å / Total num. of bins used: 20
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