+Open data
-Basic information
Entry | Database: PDB / ID: 4s1i | ||||||
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Title | Pyridoxal Kinase of Entamoeba histolytica with PLP | ||||||
Components | (Pyridoxal kinase) x 2 | ||||||
Keywords | TRANSFERASE / pyridoxal 5'-phosphate | ||||||
Function / homology | Function and homology information pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Tarique, K.F. / Devi, S. / Abdul Rehman, S.A. / Gourinath, S. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Characterization and functional insights into the Entamoeba histolytica pyridoxal kinase, an enzyme essential for its survival. Authors: Tarique, K.F. / Devi, S. / Tomar, P. / Ali, M.F. / Rehman, S.A.A. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s1i.cif.gz | 232.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s1i.ent.gz | 186.7 KB | Display | PDB format |
PDBx/mmJSON format | 4s1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/4s1i ftp://data.pdbj.org/pub/pdb/validation_reports/s1/4s1i | HTTPS FTP |
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-Related structure data
Related structure data | 4s1hC 4s1mSC S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 280 / Label seq-ID: 1 - 280
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-Components
#1: Protein | Mass: 32095.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_126090 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C4LVZ4, pyridoxal kinase | ||||
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#2: Protein | Mass: 32172.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_126090 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C4LVZ4, pyridoxal kinase | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15%Peg4000, 0.1MTris pH 7.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 74705 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Rsym value: 0.067 / Net I/σ(I): 55.27 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2.34 / Num. unique all: 3706 / Rsym value: 0.89 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4S1M Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.834 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.03 Å2
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Refine analyze | Luzzati coordinate error obs: 0.246 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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