+Open data
-Basic information
Entry | Database: PDB / ID: 1u1t | ||||||
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Title | Hfq protein from Pseudomonas aeruginosa. High-salt crystals | ||||||
Components | Hfq protein | ||||||
Keywords | RNA BINDING PROTEIN / Hfq / HF1 / Sm-like bacterial protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information regulation of carbon utilization / regulation of translation, ncRNA-mediated / regulation of RNA stability / quorum sensing / regulation of translation / regulation of DNA-templated transcription / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nikulin, A.D. / Stolboushkina, E.A. / Perederina, A.A. / Vassilieva, I.M. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. ...Nikulin, A.D. / Stolboushkina, E.A. / Perederina, A.A. / Vassilieva, I.M. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. / Nikonov, S.V. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of Pseudomonas aeruginosa Hfq protein. Authors: Nikulin, A. / Stolboushkina, E. / Perederina, A. / Vassilieva, I. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. / Nikonov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u1t.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u1t.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 1u1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u1t_validation.pdf.gz | 472 KB | Display | wwPDB validaton report |
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Full document | 1u1t_full_validation.pdf.gz | 477.6 KB | Display | |
Data in XML | 1u1t_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1u1t_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/1u1t ftp://data.pdbj.org/pub/pdb/validation_reports/u1/1u1t | HTTPS FTP |
-Related structure data
Related structure data | 1u1sC 1hk9S S: Starting model for refinement 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: 9114.487 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hfq / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q9HUM0 #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: 2.57 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1 M Li2SO4, 0.6 M ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Type: SPRING-8 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 24, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 40524 / Num. obs: 40524 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.9→2.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.8 / Num. unique all: 9200 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HK9 Resolution: 1.9→24.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3567365.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1183 Å2 / ksol: 0.371734 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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