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Yorodumi- PDB-5qog: Group deposition of apo datasets for PANDDA analysis - Crystal St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qog | ||||||
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Title | Group deposition of apo datasets for PANDDA analysis - Crystal Structure of apo EcDsbA after initial refinement (apo_dataset_9) | ||||||
Components | Thiol:disulfide interchange protein | ||||||
Keywords | OXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA | ||||||
Function / homology | Function and homology information cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.787 Å | ||||||
Authors | Ilyichova, O.V. / Bentley, M.R. / Doak, B.C. / Scanlon, M.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX). Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, ...Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, B. / Doak, B.C. / 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 | 5qog.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qog.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 5qog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/5qog ftp://data.pdbj.org/pub/pdb/validation_reports/qo/5qog | HTTPS FTP |
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-Group deposition
ID | G_1002060 (149 entries) |
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Title | Crystal Structures of EcDsbA soaked with a library of unpurified reactions after initial automated refinement |
Type | undefined |
Description | EcDsbA crystals were soaked with 93 diverse amide reactions. The structures after the initial refinement are presented in this group deposition alongside with 34 apo structures that were used in the calculations of the ground state by PANDDA |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 21155.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dsbA / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A073FPA6, UniProt: P0AEG4*PLUS #2: 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: 2.61 Å3/Da / Density % sol: 52.8 % / Mosaicity: 0.31 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 11-13% PEG 8000 5-7.5% GLYCEROL 1 MM CUCL2 100 MM SODIUM CACODYLATE |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 26, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→47.97 Å / Num. obs: 41255 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.043 / Rrim(I) all: 0.088 / Net I/σ(I): 14 / Num. measured all: 170687 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.787→34.18 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 25.13 / 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: 101.93 Å2 / Biso mean: 24.9524 Å2 / Biso min: 9.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.787→34.18 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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