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Yorodumi- PDB-6mxv: The crystal structure of a rhodanese-like family protein from Fra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mxv | ||||||
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Title | The crystal structure of a rhodanese-like family protein from Francisella tularensis subsp. tularensis SCHU S4 | ||||||
Components | Rhodanese-like family protein | ||||||
Keywords | UNKNOWN FUNCTION / Rhodanese-like family protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / DI(HYDROXYETHYL)ETHER / Rhodanese-like family protein Function and homology information | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å | ||||||
Authors | Tan, K. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The crystal structure of a rhodanese-like family protein from Francisella tularensis subsp. tularensis SCHU S4 Authors: Tan, K. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mxv.cif.gz | 214 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mxv.ent.gz | 179 KB | Display | PDB format |
PDBx/mmJSON format | 6mxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mxv_validation.pdf.gz | 713.5 KB | Display | wwPDB validaton report |
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Full document | 6mxv_full_validation.pdf.gz | 717.8 KB | Display | |
Data in XML | 6mxv_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 6mxv_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/6mxv ftp://data.pdbj.org/pub/pdb/validation_reports/mx/6mxv | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28551.299 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria) Strain: SCHU S4 / Schu 4 / Gene: FTT_1127 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q5NFU2 |
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-Non-polymers , 6 types, 355 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Chemical | ChemComp-12P / | #7: 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: 2.41 Å3/Da / Density % sol: 48.86 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG3350 25%, 0.2M MgCl2, 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97818 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2018 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97818 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→48.6 Å / Num. obs: 50307 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 15.348 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Χ2: 0.756 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.67 / Num. unique obs: 2503 / CC1/2: 0.839 / Rpim(I) all: 0.266 / Rrim(I) all: 0.56 / Χ2: 0.894 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→48.6 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→48.6 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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