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Yorodumi- PDB-4wf4: Crystal structure of E.Coli DsbA co-crystallised in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wf4 | ||||||
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Title | Crystal structure of E.Coli DsbA co-crystallised in complex with compound 4 | ||||||
Components | Thiol:disulfide interchange protein | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information disulfide oxidoreductase activity / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Adams, L.A. / Sharma, P. / Mohanty, B. / Ilyichova, O.V. / Mulcair, M.D. / Williams, M.L. / Gleeson, E.C. / Totsika, M. / Doak, B.C. / Caria, S. ...Adams, L.A. / Sharma, P. / Mohanty, B. / Ilyichova, O.V. / Mulcair, M.D. / Williams, M.L. / Gleeson, E.C. / Totsika, M. / Doak, B.C. / Caria, S. / Rimmer, K. / Shouldice, S.R. / Vazirani, M. / Headey, S.J. / Plumb, B.R. / Martin, J.L. / Heras, B. / Simpson, J.S. / Scanlon, M.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Application of Fragment-Based Screening to the Design of Inhibitors of Escherichia coli DsbA. Authors: Adams, L.A. / Sharma, P. / Mohanty, B. / Ilyichova, O.V. / Mulcair, M.D. / Williams, M.L. / Gleeson, E.C. / Totsika, M. / Doak, B.C. / Caria, S. / Rimmer, K. / Horne, J. / Shouldice, S.R. / ...Authors: Adams, L.A. / Sharma, P. / Mohanty, B. / Ilyichova, O.V. / Mulcair, M.D. / Williams, M.L. / Gleeson, E.C. / Totsika, M. / Doak, B.C. / Caria, S. / Rimmer, K. / Horne, J. / Shouldice, S.R. / Vazirani, M. / Headey, S.J. / Plumb, B.R. / Martin, J.L. / Heras, B. / Simpson, J.S. / 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 | 4wf4.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wf4.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wf4_validation.pdf.gz | 716.1 KB | Display | wwPDB validaton report |
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Full document | 4wf4_full_validation.pdf.gz | 716.2 KB | Display | |
Data in XML | 4wf4_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 4wf4_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/4wf4 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wf4 | HTTPS FTP |
-Related structure data
Related structure data | 4wetC 4weyC 4wf5C 1fvkS S: Starting model for refinement C: citing same article (ref.) |
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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: 21155.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Genus: dsbA References: UniProt: C5WBA2, UniProt: A0A0H2UL03*PLUS, protein-disulfide reductase (glutathione) #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-WF4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100-200 mM KBr, 28-33% PEG 2000 MME |
-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 |
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: 1.7→46.53 Å / Num. obs: 39824 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FVK Resolution: 1.7→36.617 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→36.617 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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