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Yorodumi- PDB-5dch: Crystal structure of Pseudomonas aeruginosa DsbA E82I in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dch | |||||||||
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Title | Crystal structure of Pseudomonas aeruginosa DsbA E82I in complex with MIPS-0000851 (3-[(2-METHYLBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-4-AMINE) | |||||||||
Components | Thiol:disulfide interchange protein DsbA | |||||||||
Keywords | OXIDOREDUCTASE / thioredoxin fold | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.447 Å | |||||||||
Authors | McMahon, R.M. / Martin, J.L. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: PLoS ONE / Year: 2017 Title: Fragment library screening identifies hits that bind to the non-catalytic surface of Pseudomonas aeruginosa DsbA1. Authors: Mohanty, B. / Rimmer, K. / McMahon, R.M. / Headey, S.J. / Vazirani, M. / Shouldice, S.R. / Coincon, M. / Tay, S. / Morton, C.J. / Simpson, J.S. / Martin, J.L. / Scanlon, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dch.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dch.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/5dch ftp://data.pdbj.org/pub/pdb/validation_reports/dc/5dch | HTTPS FTP |
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-Related structure data
Related structure data | 2mbtC 5tlqC 3h93S C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 21351.514 Da / Num. of mol.: 1 / Mutation: E82I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: dsbA, PA5489 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P0C2B2 | ||||
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#2: Chemical | ChemComp-1YO / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MES / | #5: 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: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20-29 % PEG 1500, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.447→35.1 Å / Num. obs: 31349 / % possible obs: 96.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Net I/σ(I): 14.1 / Num. measured all: 232922 / Scaling rejects: 12 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H93 Resolution: 1.447→35.098 Å / FOM work R set: 0.9076 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.25 / 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: 66.58 Å2 / Biso mean: 19.19 Å2 / Biso min: 6.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.447→35.098 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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