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Yorodumi- PDB-4exj: Crystal structure of glutathione s-transferase like protein lelg_... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4exj | ||||||
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Title | Crystal structure of glutathione s-transferase like protein lelg_03239 (target efi-501752) from lodderomyces elongisporus | ||||||
Components | uncharacterized protein | ||||||
Keywords | Structural Genomics / Unknown Function / TRANSFERASE-LIKE PROTEIN / TRANSCRIPTION REGULATION / TRANSFERASE / ENZYME FUNCTION INITIATIVE | ||||||
Function / homology | Function and homology information Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Lodderomyces elongisporus NRRL YB-4239 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of glutathione s-transferase like protein lelg_03239 (target efi-501752) from lodderomyces elongisporus Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Zencheck, W.D. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4exj.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4exj.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 4exj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4exj_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 4exj_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 4exj_validation.xml.gz | 22 KB | Display | |
Data in CIF | 4exj_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/4exj ftp://data.pdbj.org/pub/pdb/validation_reports/ex/4exj | HTTPS FTP |
-Related structure data
Related structure data | 3ay8S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28137.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lodderomyces elongisporus NRRL YB-4239 (fungus) Strain: ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239 Gene: LELG_03239 / References: UniProt: A5E0V2 #2: Chemical | #3: Chemical | #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: 2.13 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M LITHIUM SULFATE, 0.1M BIS-TRIS 25% PEG3350, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2012 / Details: MIRRORS |
Radiation | Monochromator: Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→70 Å / Num. obs: 57493 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 4.1 % / Biso Wilson estimate: 28.653 Å2 / Rsym value: 0.049 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.5 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AY8 Resolution: 1.64→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.179 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.052 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.683 Å / Total num. of bins used: 20
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