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Yorodumi- PDB-7dk9: Crystal structure of DsbA-like protein DR2335 from Deinococcus ra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dk9 | ||||||
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Title | Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein | ||||||
Components | DSBA domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / DsbA / thioredoxin fold / Thiol:disulfide interchange protein | ||||||
Function / homology | DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin-like superfamily / oxidoreductase activity / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / DSBA domain-containing protein Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å | ||||||
Authors | Kim, M.-K. / Zhang, J. / Zhao, L. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein Authors: Kim, M.-K. / Zhang, J. / Zhao, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dk9.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dk9.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/7dk9 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dk9 | HTTPS FTP |
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-Related 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: 26302.168 Da / Num. of mol.: 2 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_2335 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRZ4 #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.65 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: Sodium potassium phosphate pH 7.0, 8% w/v PEG 500 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 51343 / % possible obs: 97.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Rsym value: 0.056 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 1.72→1.75 Å / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 7.932 / Num. unique obs: 2628 / CC1/2: 0.954 / Rpim(I) all: 0.089 / Rrim(I) all: 0.204 / Rsym value: 0.182 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.72→31.51 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 20.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.46 Å2 / Biso mean: 15.6404 Å2 / Biso min: 2.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.72→31.51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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