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Yorodumi- PDB-6rng: Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rng | ||||||
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Title | Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase | ||||||
Components | Fructose-bisphosphate aldolase 6, cytosolic | ||||||
Keywords | PEPTIDE BINDING PROTEIN / ---- | ||||||
Function / homology | Function and homology information mitochondria-nucleus signaling pathway / salicylic acid binding / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / plasmodesma / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / glycolytic process / cellular response to hypoxia / copper ion binding ...mitochondria-nucleus signaling pathway / salicylic acid binding / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / plasmodesma / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / glycolytic process / cellular response to hypoxia / copper ion binding / mRNA binding / endoplasmic reticulum / mitochondrion / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Shahar, A. / Zarivach, R. / Skirycz, A. / Wojciechowska, I. | ||||||
Citation | Journal: Not Published Title: Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase Authors: Wojciechowska, I. / Vogeli, B. / Shahar, A. / Szlachetko, J. / Gorka, M. / Sokolowska, E.M. / Veyel, D. / Silva, D.V. / Erb, T. / Zarivach, R. / Skirycz, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rng.cif.gz | 509.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rng.ent.gz | 421.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/6rng ftp://data.pdbj.org/pub/pdb/validation_reports/rn/6rng | HTTPS FTP |
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-Related structure data
Related structure data | 5ky6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 38433.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FBA6, At2g36460 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q9SJQ9, fructose-bisphosphate aldolase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: 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: 2.27 Å3/Da / Density % sol: 45.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium Sulfate, 0.1 M Bis-Tris pH 6.4, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.23 Å / Num. obs: 69691 / % possible obs: 96.8 % / Redundancy: 3.6 % / Rpim(I) all: 0.088 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.15→2.23 Å / Num. unique obs: 3615 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KY6 Resolution: 2.15→46.23 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.866 / SU B: 19.687 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.471 / ESU R Free: 0.297 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.164 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→46.23 Å
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Refine LS restraints |
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