+Open data
-Basic information
Entry | Database: PDB / ID: 4e2d | ||||||
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Title | Structure of the old yellow enzyme from Trypanosoma cruzi | ||||||
Components | Old Yellow Protein | ||||||
Keywords | OXIDOREDUCTASE / TIM-barrel fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å | ||||||
Authors | Murakami, M.T. / Rodrigues, N.C. / Gava, L.M. / Canduri, F. / Oliva, G. / Barbosa, L.R.S. / Borgers, J.C. | ||||||
Citation | Journal: To be Published Title: High resolution crystal structure and in solution studies of the Old Yellow Enzyme from Trypanosoma cruzi: Insights into oligomerization, enzyme dynamics and specificity Authors: Murakami, M.T. / Rodrigues, N.C. / Gava, L.M. / Canduri, F. / Oliva, G. / Barbosa, L.R.S. / Borgers, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e2d.cif.gz | 309.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e2d.ent.gz | 251.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e2d_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4e2d_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4e2d_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 4e2d_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/4e2d ftp://data.pdbj.org/pub/pdb/validation_reports/e2/4e2d | HTTPS FTP |
-Related structure data
Related structure data | 4e2bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 42557.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TJB8 #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | |
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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: 1.96 Å3/Da / Density % sol: 37.35 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 28% (w/v) polyethylene glycol 1500, 0.3 M ammonium fluoride and 10% DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2012 | |||||||||||||||
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.46 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.997→40 Å / Num. all: 155841 / Num. obs: 80586 / % possible obs: 90.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 | |||||||||||||||
Reflection shell | Resolution: 1.997→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.251 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4E2B Resolution: 1.997→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.132 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 24.694 Å2
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Refinement step | Cycle: LAST / Resolution: 1.997→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.997→2.048 Å / Total num. of bins used: 20
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