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Yorodumi- PDB-6a4j: Crystal structure of Thioredoxin reductase 2 from Staphylococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a4j | |||||||||
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Title | Crystal structure of Thioredoxin reductase 2 from Staphylococcus aureus | |||||||||
Components | Ferredoxin--NADP reductase | |||||||||
Keywords | OXIDOREDUCTASE / flavoenzyme | |||||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | |||||||||
Authors | Bose, M. / Bhattacharyya, S. / Ghosh, A.K. / Das, A.K. | |||||||||
Funding support | India, 1items
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Citation | Journal: Biochimie / Year: 2019 Title: Elucidation of the mechanism of disulfide exchange between staphylococcal thioredoxin2 and thioredoxin reductase2: A structural insight. Authors: Bose, M. / Bhattacharyya, S. / Biswas, R. / Roychowdhury, A. / Bhattacharjee, A. / Ghosh, A.K. / Das, A.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a4j.cif.gz | 269.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a4j.ent.gz | 215.6 KB | Display | PDB format |
PDBx/mmJSON format | 6a4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a4j_validation.pdf.gz | 926.3 KB | Display | wwPDB validaton report |
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Full document | 6a4j_full_validation.pdf.gz | 938.3 KB | Display | |
Data in XML | 6a4j_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 6a4j_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a4j ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a4j | HTTPS FTP |
-Related structure data
Related structure data | 4ruvC 5twcS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 38288.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: trxB_2, EP54_04310, EQ90_00075, RK60_12235, RK64_12650, RK68_02995, RK73_09520, RK98_08250, RL06_05030, SAMEA3448991_00661 Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 References: UniProt: A0A1Q4GXS1, UniProt: Q2FVP8*PLUS, ferredoxin-NADP+ reductase #2: Chemical | |
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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: 3.3 Å3/Da / Density % sol: 62.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 28, 2017 / Details: varimax osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→19.861 Å / Num. obs: 14419 / % possible obs: 99.3 % / Redundancy: 2 % / CC1/2: 0.979 / Rmerge(I) obs: 0.1193 / Rpim(I) all: 0.1193 / Rrim(I) all: 0.1687 / Net I/σ(I): 6.01 |
Reflection shell | Resolution: 3.4→19.86 Å / Rmerge(I) obs: 0.3953 / Num. unique obs: 1427 / CC1/2: 0.658 / Rpim(I) all: 0.3953 / Rrim(I) all: 0.559 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TWC Resolution: 3.4→19.861 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→19.861 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -4.6846 Å / Origin y: 16.8835 Å / Origin z: -53.5689 Å
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Refinement TLS group | Selection details: all |