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Yorodumi- PDB-2pfs: Crystal structure of universal stress protein from Nitrosomonas e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pfs | ||||||
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Title | Crystal structure of universal stress protein from Nitrosomonas europaea | ||||||
Components | Universal stress protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / stress protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nitrosomonas europaea ATCC 19718 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Chruszcz, M. / Evdokimova, E. / Cymborowski, M. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Evol Appl / Year: 2013 Title: Structural and functional insight into the universal stress protein family. Authors: Tkaczuk, K.L. / Shumilin, I.A. / Chruszcz, M. / Evdokimova, E. / Savchenko, A. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pfs.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pfs.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pfs_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 2pfs_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 2pfs_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 2pfs_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pfs ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pfs | HTTPS FTP |
-Related structure data
Related structure data | 3qtbC 3tnjC 6hcdC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16756.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria) Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: NE1028 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q82VN8 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.2M Sodium chloride, 0.1M HEPES pH 7.5, 25% PEG3350, 2% Isopropanol, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 6882 / Num. obs: 6882 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 58.5 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / Num. unique all: 277 / Rsym value: 0.486 / % possible all: 81.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.231 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.277 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.309 Å / Total num. of bins used: 20
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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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