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Yorodumi- PDB-6rs1: Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rs1 | ||||||
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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: 1.9 Å | ||||||
Authors | Shahar, A. / Zarivach, R. / Skirycz, A. / Wojciechowska, I. | ||||||
Citation | Journal: To Be 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 | 6rs1.cif.gz | 516.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rs1.ent.gz | 426.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rs1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rs1_validation.pdf.gz | 474.8 KB | Display | wwPDB validaton report |
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Full document | 6rs1_full_validation.pdf.gz | 500 KB | Display | |
Data in XML | 6rs1_validation.xml.gz | 54.3 KB | Display | |
Data in CIF | 6rs1_validation.cif.gz | 77.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/6rs1 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/6rs1 | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 4 - 340 / Label seq-ID: 4 - 340
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: 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: 2.3 Å3/Da / Density % sol: 46.48 % |
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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 6.2 and 25% 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: 1.072 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: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.37 Å / Num. obs: 88957 / % possible obs: 83.45 % / Redundancy: 4.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.09 / Rrim(I) all: 0.2 / Net I/σ(I): 7.04 |
Reflection shell | Resolution: 1.9→2.04 Å / Rmerge(I) obs: 1.194 / Num. unique obs: 4572 / CC1/2: 0.623 / Rpim(I) all: 0.6 / Rrim(I) all: 1.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KY6 Resolution: 1.9→48.37 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.687 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.212 / 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: 20.153 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.37 Å
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Refine LS restraints |
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