+Open data
-Basic information
Entry | Database: PDB / ID: 2o67 | ||||||
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Title | Crystal structure of Arabidopsis thaliana PII bound to malonate | ||||||
Components | PII protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / REGULATION OF NITROGEN AND CARBON METABOLISM | ||||||
Function / homology | Function and homology information acetylglutamate kinase regulator activity / regulation of arginine biosynthetic process via ornithine / anthocyanin-containing compound biosynthetic process / chloroplast thylakoid / response to sucrose / regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / : / plastid / response to light stimulus ...acetylglutamate kinase regulator activity / regulation of arginine biosynthetic process via ornithine / anthocyanin-containing compound biosynthetic process / chloroplast thylakoid / response to sucrose / regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / : / plastid / response to light stimulus / chloroplast / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mizuno, Y.M. / Berenger, B. / Moorhead, G.B.G. / Ng, K.K.S. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structure of Arabidopsis PII Reveals Novel Structural Elements Unique to Plants. Authors: Mizuno, Y. / Berenger, B. / Moorhead, G.B. / Ng, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o67.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o67.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 2o67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/2o67 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/2o67 | HTTPS FTP |
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-Related structure data
Related structure data | 2o66SC 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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Details | Native homotrimer is found in the asymmetric unit |
-Components
#1: Protein | Mass: 14779.914 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g01900, T7B11.16 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami pLysS / References: UniProt: Q9ZST4 #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: 1.88 Å3/Da / Density % sol: 34.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.5 M malonate, 0.1 M Na HEPES, pH 7.0, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2006 / Details: Osmic multilayer |
Radiation | Monochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 11464 / Num. obs: 11464 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1139 / Rsym value: 0.517 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2O66 Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.716 / SU ML: 0.262 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.914 / ESU R Free: 0.326 / Stereochemistry target values: Engh & Huber
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.622 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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