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Yorodumi- PDB-4co0: Structure of PII signaling protein GlnZ from Azospirillum brasile... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4co0 | ||||||
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Title | Structure of PII signaling protein GlnZ from Azospirillum brasilense in complex with adenosine diphosphate | ||||||
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: 1.4 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 | 4co0.cif.gz | 104.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4co0.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 4co0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4co0 ftp://data.pdbj.org/pub/pdb/validation_reports/co/4co0 | HTTPS FTP |
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-Related structure data
Related structure data | 4cnySC 4cnzC 4co1C 4co2C 4co3C 4co4C 4co5C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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.: 2 / Source method: isolated from a natural source / Source: (natural) AZOSPIRILLUM BRASILENSE (bacteria) / References: UniProt: P70731 #2: Chemical | #3: Chemical | ChemComp-TLA / | #4: 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: 1.91 Å3/Da / Density % sol: 35.73 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1 MM MNCL2, 5MM 2OG, 5 MMATP, 0.2 M K/NA TARTRATE, 200% PEG 3350, 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: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2009 Details: VERTICALLY COLLIMATING MIRROR FOLLOWED BY A BARTELS MONOCHROMATOR AND TOROIDAL MIRROR |
Radiation | Monochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→29.87 Å / Num. obs: 35124 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 5.33 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CNY Resolution: 1.4→29.868 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 23.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.083 Å2 / ksol: 0.342 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→29.868 Å
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Refine LS restraints |
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LS refinement shell |
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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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