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Yorodumi- PDB-7s2p: Crystal structure of the F337L mutation of Trypanosoma cruzi gluc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s2p | ||||||
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Title | Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in complex with inhibitor CBZ-GlcN | ||||||
Components | Glucokinase 1 | ||||||
Keywords | TRANSFERASE / Trypanosoma cruzi / Chagas disease | ||||||
Function / homology | Function and homology information glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Carey, S.M. / Nettles, R.B. / Daneshian, L. / Chruszcz, M. / D'Antonio, E.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the F337L mutation of Trypanosoma cruzi glucokinase in complex with inhibitor CBZ-GlcN Authors: Carey, S.M. / Nettles, R.B. / Daneshian, L. / 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 | 7s2p.cif.gz | 299.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s2p.ent.gz | 244 KB | Display | PDB format |
PDBx/mmJSON format | 7s2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s2p_validation.pdf.gz | 1017.7 KB | Display | wwPDB validaton report |
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Full document | 7s2p_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7s2p_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 7s2p_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/7s2p ftp://data.pdbj.org/pub/pdb/validation_reports/s2/7s2p | HTTPS FTP |
-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: _ / 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: _ / Auth seq-ID: 1 - 365 / Label seq-ID: 15 - 379
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-Components
#1: Protein | Mass: 42192.633 Da / Num. of mol.: 2 / Mutation: F337L 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: Sugar | #3: Chemical | ChemComp-SO4 / | #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: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: A ligand-free TcGlcK(F337L) crystal was soaked in 1.0 mM CBZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 15% (w/v) PEG 3,350 for 24 hours |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→40 Å / Num. obs: 33656 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1666 / CC1/2: 0.702 / Rpim(I) all: 0.372 / Rrim(I) all: 0.718 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q2R Resolution: 2.35→38.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.396 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.259 / 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: 160.77 Å2 / Biso mean: 71.278 Å2 / Biso min: 40.05 Å2
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Refinement step | Cycle: final / Resolution: 2.35→38.4 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 11026 / 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: 2.35→2.411 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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