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Yorodumi- PDB-5id4: Crystal structure of Proteus mirabilis ScsC in an extended confor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5id4 | ||||||
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Title | Crystal structure of Proteus mirabilis ScsC in an extended conformation | ||||||
Components | DsbA-like protein | ||||||
Keywords | ISOMERASE / thioredoxin fold / disulfide isomerase / trimer / copper resistance | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Proteus mirabilis ATCC 29906 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.921 Å | ||||||
Authors | Furlong, E.J. / Kurth, F. / Choudhury, H.G. / Martin, J.L. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Proteus mirabilis ScsC is a highly dynamic, novel trimeric protein disulfide isomerase Authors: Kurth, F. / Furlong, E.J. / Lo, A.W. / Premkumar, L. / Totsika, M. / Whitten, A.E. / Achard, M.E.S. / Halili, M.A. / Heras, B. / Choudhury, H.G. / Schembri, M.A. / Martin, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5id4.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5id4.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 5id4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5id4_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 5id4_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 5id4_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 5id4_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/5id4 ftp://data.pdbj.org/pub/pdb/validation_reports/id/5id4 | HTTPS FTP |
-Related structure data
Related structure data | 4yx8 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: 24800.443 Da / Num. of mol.: 1 / Fragment: UNP residues 22-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis ATCC 29906 (bacteria) Gene: HMPREF0693_3732 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C2LPE2 |
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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: 4.83 Å3/Da / Density % sol: 74.53 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 32% Jeffamine M-600 pH 7, 0.1 M HEPES pH 8, 2.5 mM Copper(II) chloride PH range: 7-8 |
-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: Dec 10, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.92→110.29 Å / Num. obs: 10755 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 85.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.033 / Rrim(I) all: 0.068 / Net I/σ(I): 14.2 / Num. measured all: 44513 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YX8 4yx8 Resolution: 2.921→40.363 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3 / 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: 214.71 Å2 / Biso mean: 108.8807 Å2 / Biso min: 9.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.921→40.363 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: 4
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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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