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Yorodumi- PDB-8czn: Crystal Structure of EcDsbA in a complex with 1H-pyrrole-3-carbox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8czn | |||||||||
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Title | Crystal Structure of EcDsbA in a complex with 1H-pyrrole-3-carboxylic acid | |||||||||
Components | Thiol:disulfide interchange protein DsbA | |||||||||
Keywords | OXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / Microfrag screening / FBDD / Fragment | |||||||||
Function / homology | Function and homology information cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Whitehouse, R.L. / Ilyichova, O.V. / Taylor, A.J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Rsc Med Chem / Year: 2023 Title: Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores. Authors: Whitehouse, R.L. / Alwan, W.S. / Ilyichova, O.V. / Taylor, A.J. / Chandrashekaran, I.R. / Mohanty, 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 | 8czn.cif.gz | 206.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8czn.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 8czn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/8czn ftp://data.pdbj.org/pub/pdb/validation_reports/cz/8czn | HTTPS FTP |
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-Related structure data
Related structure data | 8cxdC 8cxeC 8czmC 8d10C 8d11C 8d12C 8dg0C 8dg1C 8dg2C 1fvkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.965607807855, 0.0637850787006, 0.252057582994), (-0.251770538593, 0.0126309586466, -0.967704528655), (-0.0649088384265, -0.997883721993, 0.00386265132877)Vector: 36. ...NCS oper: (Code: given Matrix: (-0.965607807855, 0.0637850787006, 0.252057582994), Vector: |
-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) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4 #2: Chemical | ChemComp-PKN / #3: Chemical | ChemComp-CU / | #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: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 11-13 % PEG 8000, 5-7.5% GLYCEROL, 100MM NA CACODYLATE PH6.1, 1MM CuCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95365 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→48.14 Å / Num. obs: 62171 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Χ2: 0.5 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.59→1.61 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.726 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2545 / CC1/2: 0.369 / Rpim(I) all: 0.821 / Χ2: 0.369 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FVK Resolution: 1.7→31.6 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.3131 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 27.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→31.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.0782598151 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 19.9043326833 Å / Origin y: 0.102637454795 Å / Origin z: 14.2727659789 Å
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Refinement TLS group | Selection details: all |