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Yorodumi- PDB-2y3y: Holo-Ni(II) HpNikR is a symmetric tetramer containing four canoni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y3y | ||||||
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Title | Holo-Ni(II) HpNikR is a symmetric tetramer containing four canonic square-planar Ni(II) ions at physiological pH | ||||||
Components |
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Keywords | TRANSCRIPTION / METAL BINDING | ||||||
Function / homology | Function and homology information response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI G27 (bacteria) UNIDENTIFIED (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å | ||||||
Authors | Benini, S. / Cianci, M. / Ciurli, S. | ||||||
Citation | Journal: Dalton Trans / Year: 2011 Title: Holo-Ni(2+)Helicobacter Pylori Nikr Contains Four Square-Planar Nickel-Binding Sites at Physiological Ph. Authors: Benini, S. / Cianci, M. / Ciurli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y3y.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y3y.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 2y3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/2y3y ftp://data.pdbj.org/pub/pdb/validation_reports/y3/2y3y | 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 5 molecules ABCDQ
#1: Protein | Mass: 10428.796 Da / Num. of mol.: 4 / Fragment: C-TERMINAL METAL-BINDING DOMAIN, RESIDUES 58-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI G27 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5Z8Y5 #2: Protein/peptide | | Mass: 823.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) UNIDENTIFIED (others) |
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-Non-polymers , 4 types, 75 molecules
#3: Chemical | ChemComp-NI / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | ONLY C-TERMINAL METAL-BINDING DOMAIN PRESENT. |
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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: 4.05 Å3/Da / Density % sol: 69.64 % / Description: NONE |
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Crystal grow | pH: 7.3 / Details: 20% PEG 3350 AND 0.2 M K/NA-TARTRATE, pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.459 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→19.94 Å / Num. obs: 24202 / % possible obs: 99.8 % / Observed criterion σ(I): 3.5 / Redundancy: 14 % / Biso Wilson estimate: 52.396 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2.39→2.52 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.39→72.98 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / SU B: 6.966 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. UNEXPECTED ELECTRON DENSITY WAS MODELED AS ALPHA-CHAIN (Q)
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.377 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→72.98 Å
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