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Yorodumi- PDB-4co1: Structure of PII signaling protein GlnZ from Azospirillum brasile... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4co1 | ||||||
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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: 1.5 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 | 4co1.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4co1.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 4co1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4co1 ftp://data.pdbj.org/pub/pdb/validation_reports/co/4co1 | HTTPS FTP |
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-Related structure data
Related structure data | 4cnySC 4cnzC 4co0C 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: 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: 2.11 Å3/Da / Density % sol: 41.81 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 MM ADP, 0.1 M NA HEPES PH 7.5, 25% PEG 1000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-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: May 3, 2009 Details: VERTICALLY COLLIMATING MIRROR FOLLOWED BY A BARTELS MONOCHROMATOR AND A 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 twin | Operator: h,-h-k,-l / Fraction: 0.45 |
Reflection | Resolution: 1.5→30.9 Å / Num. obs: 32015 / % possible obs: 88.5 % / Observed criterion σ(I): 2 / Redundancy: 5.32 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 4.78 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CNY Resolution: 1.5→30.89 Å / σ(F): 2.01 / Phase error: 21.67 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.275 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30.89 Å
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Refine LS restraints |
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LS refinement shell |
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