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Yorodumi- PDB-4aec: Crystal Structure of the Arabidopsis thaliana O-Acetyl-Serine-(Th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aec | ||||||
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Title | Crystal Structure of the Arabidopsis thaliana O-Acetyl-Serine-(Thiol)- Lyase C | ||||||
Components | CYSTEINE SYNTHASE, MITOCHONDRIAL | ||||||
Keywords | LYASE / CYSTEINE SYNTHESIS / ASSIMILATORY SULFATE REDUCTION / SULFIDE / PLANT INORGANIC SULFUR UPTAKE | ||||||
Function / homology | Function and homology information double fertilization forming a zygote and endosperm / pollen tube growth / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / mitochondrion / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Feldman-Salit, A. / Wirtz, M. / Lenherr, E.D. / Throm, C. / Hothorn, M. / Scheffzek, K. / Hell, R. / Wade, R.C. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Allosterically Gated Enzyme Dynamics in the Cysteine Synthase Complex Regulate Cysteine Biosynthesis in Arabidopsis Thaliana. Authors: Feldman-Salit, A. / Wirtz, M. / Lenherr, E.D. / Throm, C. / Hothorn, M. / Scheffzek, K. / Hell, R. / Wade, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aec.cif.gz | 258.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aec.ent.gz | 209.6 KB | Display | PDB format |
PDBx/mmJSON format | 4aec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/4aec ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4aec | HTTPS FTP |
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-Related structure data
Related structure data | 1z7wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45864.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q43725, cysteine synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #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: 2.26 Å3/Da / Density % sol: 45.07 % / Description: NONE |
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Crystal grow | Temperature: 291 K Details: 18C, 1:1 15MG/ML PROTEIN MIXED WITH: 28% PEG 8000 100 MM MES, PH 6.5 300 MM NA ACETATE SUPPLEMENTED BY 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97297 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97297 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 24684 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 6.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z7W Resolution: 2.4→19.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.568 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.281 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.94 Å
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Refine LS restraints |
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