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Yorodumi- PDB-5xwh: Structure of FrnE, a novel disulfide oxidoreductase from Deinococ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xwh | ||||||
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Title | Structure of FrnE, a novel disulfide oxidoreductase from Deinococcus radiodurans crystallized in the presence of GSH | ||||||
Components | FrnE protein | ||||||
Keywords | OXIDOREDUCTASE / Disulfide oxidoreductase / Disulfide isomerase / FrnE | ||||||
Function / homology | DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / oxidoreductase activity / 3-Layer(aba) Sandwich / Alpha Beta / FrnE protein Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bihani, S.C. / Panicker, L. / Kumar, V. | ||||||
Citation | Journal: To Be Published Title: Structure of FrnE, a novel disulfide oxidoreductase from Deinococcus radiodurans crystallized in the presence of GSH Authors: Bihani, S.C. / Panicker, L. / Kumar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xwh.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xwh.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xwh_validation.pdf.gz | 427.8 KB | Display | wwPDB validaton report |
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Full document | 5xwh_full_validation.pdf.gz | 429 KB | Display | |
Data in XML | 5xwh_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 5xwh_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/5xwh ftp://data.pdbj.org/pub/pdb/validation_reports/xw/5xwh | HTTPS FTP |
-Related structure data
Related structure data | 5co3S 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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Details | Authors state that dimeric biological assembly is observed in solution using SEC and light scattering experiment. |
-Components
#1: Protein | Mass: 28493.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_0659 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RWK7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 10% PEG8000, 100mM sodium acetate, pH 5.0 20% glycerol 5mM GSH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.81 Å / Num. obs: 17317 / % possible obs: 94.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.427 / CC1/2: 0.745 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CO3 Resolution: 2→41.822 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 23.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.822 Å
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Refine LS restraints |
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LS refinement shell |
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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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