[English] 日本語
Yorodumi- PDB-6w49: Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC010) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w49 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC010) | ||||||||||||
Components | Malic enzyme | ||||||||||||
Keywords | OXIDOREDUCTASE/Inhibitor / Inhibitor / complex / isomerase / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex | ||||||||||||
Function / homology | Function and homology information malate dehydrogenase (decarboxylating) (NAD+) activity / malate metabolic process / pyruvate metabolic process / NAD binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Mercaldi, G.F. / Fagundes, M. / Faria, J.N. / Cordeiro, A.T. | ||||||||||||
Funding support | Brazil, 3items
| ||||||||||||
Citation | Journal: Acs Infect Dis. / Year: 2021 Title: Trypanosoma cruzi Malic Enzyme Is the Target for Sulfonamide Hits from the GSK Chagas Box. Authors: Mercaldi, G.F. / Eufrasio, A.G. / Ranzani, A.T. / do Nascimento Faria, J. / Mota, S.G.R. / Fagundes, M. / Bruder, M. / Cordeiro, A.T. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6w49.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6w49.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 6w49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w49_validation.pdf.gz | 774.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6w49_full_validation.pdf.gz | 777.5 KB | Display | |
Data in XML | 6w49_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 6w49_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/6w49 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w49 | HTTPS FTP |
-Related structure data
Related structure data | 6w29SC 6w2nC 6w53C 6w56C 6w57C 6w59C 7mf4C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 61610.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_11g406 / Plasmid: pET_SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2XFZ1 |
---|---|
#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-SWV / ~{ |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.56 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 1.2-1.4 M Na3-Citrate / PH range: 6.8 - 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.73 Å / Num. obs: 72505 / % possible obs: 99.9 % / Redundancy: 11.7 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.593 / Num. measured all: 24320 / Num. unique obs: 3730 / CC1/2: 0.831 / Rpim(I) all: 0.243 / Rrim(I) all: 0.643 / Net I/σ(I) obs: 2.7 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W29 Resolution: 1.7→47.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.769 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0912 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.18 Å2 / Biso mean: 22.367 Å2 / Biso min: 11.72 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→47.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|