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Yorodumi- PDB-7s2h: Crystal structure of Trypanosoma cruzi glucokinase in the apo for... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s2h | ||||||
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Title | Crystal structure of Trypanosoma cruzi glucokinase in the apo form (open conformation) | ||||||
Components | Glucokinase 1, putative | ||||||
Keywords | TRANSFERASE / Trypanosoma cruzi / Chagas disease | ||||||
Function / homology | Function and homology information glucokinase / glucokinase activity / glucose binding / glycolytic process / ATP binding Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kearns, S.P. / Daneshian, L. / Swartz, P.D. / Carey, S.M. / Chruszcz, M. / D'Antonio, E.L. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of Trypanosoma cruzi glucokinase in the apo form (open conformation) Authors: Kearns, S.P. / Daneshian, L. / Swartz, P.D. / Carey, S.M. / Chruszcz, M. / D'Antonio, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s2h.cif.gz | 303.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s2h.ent.gz | 242.6 KB | Display | PDB format |
PDBx/mmJSON format | 7s2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/7s2h ftp://data.pdbj.org/pub/pdb/validation_reports/s2/7s2h | HTTPS FTP |
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-Related structure data
Related structure data | 2q2rS 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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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: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: -1 - 365 / Label seq-ID: 13 - 379
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-Components
#1: Protein | Mass: 42226.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053510187.100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E4E1, glucokinase #2: Chemical | ChemComp-FLC / | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.0 uL of 7.4 mg/mL wt-TcGlcK in buffered solution [50 mM HEPES (pH 7.5), 0.2 M imidazole, 2 mM magnesium chloride] + 1.0 uL of precipitant solution [14% (w/v) PEG 3350, 0.1 M sodium citrate ...Details: 1.0 uL of 7.4 mg/mL wt-TcGlcK in buffered solution [50 mM HEPES (pH 7.5), 0.2 M imidazole, 2 mM magnesium chloride] + 1.0 uL of precipitant solution [14% (w/v) PEG 3350, 0.1 M sodium citrate tribasic] was equilibrated against 85 uL of the precipitant solution using a 96-well sitting-drop plate (Innovadyne) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 72625 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Net I/σ(I): 41.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3637 / CC1/2: 0.833 / Rpim(I) all: 0.344 / Rrim(I) all: 0.949 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q2R Resolution: 1.8→35.92 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.244 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 114.22 Å2 / Biso mean: 33.742 Å2 / Biso min: 20.92 Å2
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Refinement step | Cycle: final / Resolution: 1.8→35.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 11228 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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