+Open data
-Basic information
Entry | Database: PDB / ID: 5guq | ||||||
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Title | Crystal structure of ASCH from Zymomonas mobilis | ||||||
Components | Helix-turn-helix domain-containing protein | ||||||
Keywords | HYDROLASE / nuclease | ||||||
Function / homology | ASCH domain / ASCH domain / exonuclease activity / PUA-like superfamily / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / ASCH domain-containing ribonuclease Function and homology information | ||||||
Biological species | Zymomonas mobilis subsp. mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.697 Å | ||||||
Authors | Ha, S.C. / Park, S.Y. / Kim, J.S. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Crystal structure of an ASCH protein from Zymomonas mobilis and its ribonuclease activity specific for single-stranded RNA. Authors: Kim, B.N. / Shin, M. / Ha, S.C. / Park, S.Y. / Seo, P.W. / Hofmann, A. / Kim, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5guq.cif.gz | 272.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5guq.ent.gz | 223.8 KB | Display | PDB format |
PDBx/mmJSON format | 5guq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5guq ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5guq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 17303.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1) (bacteria) Strain: ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1 Gene: Zmob_0380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3G0N3 #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: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350, 0.1M MES (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.697→30.6 Å / Num. obs: 68764 / % possible obs: 98.7 % / Redundancy: 3.4 % / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Resolution: 1.697→30.592 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.697→30.592 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -32.7342 Å / Origin y: -4.2284 Å / Origin z: -19.5975 Å
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Refinement TLS group | Selection details: all |