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Yorodumi- PDB-4cny: Structure of PII signaling protein GlnZ from Azospirillum brasilense -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cny | ||||||
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Title | Structure of PII signaling protein GlnZ from Azospirillum brasilense | ||||||
Components | PII-LIKE PROTEIN PZ | ||||||
Keywords | SIGNALING PROTEIN / GLNK-LIKE | ||||||
Function / homology | Function and homology information regulation of nitrogen utilization / enzyme regulator activity / ATP binding Similarity search - Function | ||||||
Biological species | AZOSPIRILLUM BRASILENSE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Truan, D. / Li, X.-D. / Winkler, F.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structure and Thermodynamics of Effector Molecule Binding to the Nitrogen Signal Transduction Pii Protein Glnz from Azospirillum Brasilense. Authors: Truan, D. / Bjelic, S. / Li, X. / Winkler, F.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cny.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cny.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cny ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cny | HTTPS FTP |
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-Related structure data
Related structure data | 4cnzC 4co0C 4co1C 4co2C 4co3C 4co4C 4co5C 1gnkS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12287.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AZOSPIRILLUM BRASILENSE (bacteria) / References: UniProt: P70731 | ||
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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.4 M AMMONIUM PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2008 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→35.78 Å / Num. obs: 44969 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.59 % / Biso Wilson estimate: 12.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GNK Resolution: 1.2→35.775 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 12.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.208 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→35.775 Å
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Refine LS restraints |
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LS refinement shell |
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