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Yorodumi- PDB-2pln: Crystal structure analysis of HP1043, an orphan resonse regulator... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pln | ||||||
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Title | Crystal structure analysis of HP1043, an orphan resonse regulator of h. pylori | ||||||
Components | Response regulator | ||||||
Keywords | SIGNALING PROTEIN / HP1043 | ||||||
Function / homology | Function and homology information phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Lee, H.M. / Kim, D.U. / Byun, J.S. / Cho, H.S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure Analysis of Hp1043, an Orphan Resonse Regulator of H. Pylori Authors: Lee, H.M. / Hong, E. / Kim, D.U. / Byun, J.S. / Lee, W. / Cho, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pln.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pln.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/2pln ftp://data.pdbj.org/pub/pdb/validation_reports/pl/2pln | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 15662.956 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25684 |
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#2: 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: 1.86 Å3/Da / Density % sol: 34.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8K 3%, 100MM MES, 200MM CA-CACODYLATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9794 / Wavelength: 0.97940, 0.97952, 0.97962, 0.98742 | |||||||||||||||
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: May 15, 2005 | |||||||||||||||
Radiation | Monochromator: SILICONE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 11373 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.099 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rsym value: 0.368 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→44.5 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.436 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.134 / 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: 21.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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